Modulation of ire1

ABSTRACT

Described herein, inter alia, are compositions and methods of using the same for modulating the activity of Ire1.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/149,606, filed Oct. 2, 2018, which is a continuation of U.S. patentapplication Ser. No. 14/670,088, filed Mar. 26, 2015, which issued asU.S. Pat. No. 10,131,668 on Nov. 20, 2018 and which is a continuation ofInternational Application No. PCT/US2013/062039 filed Sep. 26, 2013,which in turn claims the benefit of U.S. Provisional Patent ApplicationNos. 61/706,037, filed Sep. 26, 2012; 61/783,965, filed Mar. 14, 2013;and 61/831,088, filed Jun. 4, 2013, which are all incorporated herein byreference in their entirety and for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

This invention was made with Government Support under Grant nos. R01GM086858, R01 DK080955, R01 CA136577, OD001925, and OD001926 awarded bythe National Institutes of Health. The government has certain rights inthe invention.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAMLISTING APPENDIX SUBMITTED AS AN ASCII FILE

The Sequence Listing written in file 048536-547C03US_ST25.TXT, createdon Jul. 28, 2020, 24,471 bytes, machine format IBM-PC, MS-Windowsoperating system, is hereby incorporated by reference.

BACKGROUND

Cells often experience conditions during which the workload on theendoplasmic reticulum (“ER”) protein folding machinery exceeds itscapability. Such cells are said to be experiencing “ER stress.” ERstress can result from secretory work overload, expression offolding-defective secretory proteins, deprivation of nutrients oroxygen, changes in luminal calcium concentration, and deviation fromresting redox state. Sophisticated cellular surveillance and qualitycontrol systems work to maintain ER homeostasis under suchperturbations. Under ER stress, secretory proteins accumulate inunfolded forms within the organelle to trigger a set of intracellularsignaling pathways called the unfolded protein response (UPR). UPRsignaling increases transcription of genes encoding chaperones,oxidoreductases, lipid-biosynthetic enzymes, and ER-associateddegradation (ERAD) components (Travers, K. J. et al. Cell 101, 249-258(2000)).

In some instances, the ER stressed state remains too great, and cannotbe remedied through the UPR's homeostatic outputs. In these situations,the UPR switches strategies and actively triggers apoptosis (Zhang, K. &Kaufman, R. J. Neurology 66, S102-109 (2006)); we have named thisdestructive signaling state the Terminal UPR (signature events of theTerminal UPR are described herein). Apoptosis of irremediably stressedcells is an extreme, yet definitive, quality control strategy thatprotects multicellular organisms from exposure to immature and damagedsecretory proteins. So at the cost of losing some cells, multicellularorganisms may benefit temporarily from Terminal UPR-induced apoptosis.However, many deadly human diseases occur if too many cells die throughthis process. Conversely, many human diseases such as diabetes mellitusand retinopathies proceed from unchecked cell degeneration under ERstress (Merksamer, P. I., and Papa, F. R., J Cell Sci 123, 1003-1006(2010); Papa, F. R. Cold Spring Harbor perspectives in medicine 2,a007666 (2012); Shore, G. C., Papa, F. R., and Oakes, S. A., Curr OpinCell Biol 23, 143-149 (2011)). Type 2 diabetes may be a prototype ofcell degenerative diseases caused by UPR-mediated apoptosis underirremediable ER stress. These same principles appear to be at play intype 1 diabetes, wherein immune attack on islet β-cells elevates ERworkload and causes ER stress in remaining cells. A deeper fundamentaland mechanistic understanding of the etiology and pathogenesis ofdiabetes mellitus may lead to increasing opportunities for thedevelopment of novel and effective therapies. Terminal UPR signaling iscentral to these conditions as shown through experimental data and usesof proprietary compounds that defeat the consequences of terminal UPRsignaling in ER stress-challenged β-cells to afford significantcytoprotection.

IRE1α and IRE1β are ER-transmembrane proteins that become activated whenunfolded proteins accumulate within the organelle. IRE1α is the morewidely expressed and well-studied family member. The bifunctionalkinase/endoribonuclease IRE1α controls entry into the terminal UPR.IRE1α senses unfolded proteins through an ER lumenal domain that becomesoligomerized during stress (Zhou, J. et al. Proceedings of the NationalAcademy of Sciences of the United States of America 103, 14343-14348(2006); Credle, J. J. et al. Proc Natl Acad Sci USA 102, 18773-18784(2005); Aragon, T. et al. Nature (2008); Aragon, T. et al. Nature 457,736-740 (2009)). On its cytosolic face, IRE1α possesses bifunctionalkinase/RNase activities. Oligomerization juxtaposes IRE1α's kinasedomains, which consequently trans-autophosphorylate. Kinaseautophosphorylation activates the RNase activity, which cleaves XBP1mRNA at specific sites to excise an intron. Religation of IRE1α-cleavedXBP1 mRNA shifts the open reading frame; translation of spliced XBP1mRNA produces a transcription factor called XBP1s (s=spliced) (Calfon,M. et al. Nature 415, 92-96, (2002); Yoshida, H. Cell 107, 881-891(2001)). XBP1s's target genes encode products that enhance ER proteinfolding and quality control (Lee, A. H. et al., Molecular and cellularbiology 23, 7448-7459 (2003)). Thus, IRE1α promotes adaptation viaXBP1s.

Under irremediable ER stress, positive feedback signals emanate from theUPR and become integrated and amplified at key nodes to triggerapoptosis. IRE1α is a key initiator of these pro-apoptotic signals.IRE1α employs auto-phosphorylation as a “timer.” Remediable ER stresscauses low-level, transient auto-phosphorylation that confines RNaseactivity to XBP1 mRNA splicing. However, sustained kinaseautophosphorylation causes IRE1α's RNase to acquire relaxed specificity,causing it to endonucleolytically degrade thousands of ER-localizedmRNAs in close proximity to IRE1α (Han, D. et al. Cell 138, 562-575,(2009); Hollien, J. et al. Journal of Cell Biology. These mRNAs encodesecretory proteins being co-translationally translocated (e.g., insulinin β cells). As mRNA degradation continues, transcripts encodingER-resident enzymes also become depleted, thus destabilizing the entireER protein-folding machinery. Once IRE1α's RNase becomes hyperactive,adaptive signaling through XBP1 splicing becomes eclipsed by ER mRNAdestruction, which pushes cells into apoptosis.

A terminal UPR signature tightly controlled by IRE1α's hyperactive RNaseactivity causes (1) widespread mRNA degradation at the ER membrane thatleads to mitochondrial apoptosis (Han, D. et al. Cell 138, 562-575,(2009)), (2) induction of the pro-oxidant thioredoxin-interactingprotein (TXNIP), which activates the NLRP3 inflammasome to producematuration and secretion of interleukin-1β, and consequent sterileinflammation in pancreatic islets leading to diabetes (Lerner, A. G. etal. Cell metabolism 16, 250-264, (2012)), and (3) degradation ofpre-miRNA 17, leading to translational upregulation and cleavage ofpre-mitochondrial caspase 2 (Upton, J. P. et al. Science 338, 818-822,(2012)) and stabilization of the mRNA encoding TXNIP (Lerner, A. G. etal. Cell metabolism 16, 250-264, (2012)).

Retinitis pigmentosa (RP) is a clinically and genetically heterogeneousgroup of inherited retinal disorders characterized by diffuseprogressive dysfunction and loss of rod and cone photoreceptors, andretinal pigment epithelium. There are no approved therapies to offer theover 100,000 Americans who currently suffer from RP. As RP is a leadingcause of irreversible vision loss, new therapeutic approaches for thiscondition would be expected to have significant cost-saving benefits forhealth care systems.

A great deal of evidence suggests that the accumulation of misfoldedproteins within the ER is a central causative mechanism in many forms ofRP. When the protein-folding capacity of the ER is overwhelmed, cellsexperience “ER stress” and actively commit programmed cell death. Forexample, mutations in rhodopsin are the most common cause of RP in theUS and lead to a defective rhodopsin protein that misfolds andaccumulates in the ER to cause high levels ER stress.

Disclosed herein, inter alia, are solutions to these and other problemsin the art.

BRIEF SUMMARY

Provided herein, inter alia, are novel ATP-competitive small moleculekinase inhibitors of IRE1α that prevent oligomerization and/orallosterically inhibit its RNase activity.

In an aspect is provided a compound, or a pharmaceutically acceptablesalt thereof, having the formula:

wherein, ring A is substituted or unsubstituted cycloalkylene,substituted or unsubstituted heterocycloalkylene, substituted orunsubstituted arylene, or substituted or unsubstituted heteroarylene; L¹is a bond or unsubstituted C₁-C₅ alkylene; L² is a bond, —NR^(6a)—, —O—,—S—, —C(O)—,—S(O)—, —S(O)₂—, —NR^(6a)C(O)—, —C(O)(CH₂)_(z2)—, —C(O)NR^(6b)—,—NR^(6a)C(O)O—, —NR^(6a)C(O)NR^(6b)—, substituted or unsubstitutedalkylene, substituted or unsubstituted heteroalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene; R¹ is hydrogen, oxo,halogen, —CX₃, —CN, —SO₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO_(n)R¹⁰, —NR^(7b)C═(O)R⁹, —NR^(7b)C(O)OR⁹,—NR⁷OR⁹, —OCX₃, —OCHX₂, substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R² ishydrogen, oxo,halogen, —CX^(a) ₃, —CN, —SO₂Cl, —SO_(n1)R^(10a), —SO_(v1)NR^(7a)R^(8a),—NHNH₂, —ONR^(7a)R^(8a), —NHC═(O)NHNH₂, —NHC═(O)NR^(7a)R^(8a),—N(O)_(m1), —NR^(7a)R^(8a), —C(O)R^(9a), —C(O)OR^(9a),—C(O)NR^(7a)R^(8a), —OR^(10a), —NR^(7a)SO_(n1)R^(10a),—NR^(7a)C═(O)R^(9a), —NR^(7a)C(O)OR^(9a), —NR^(7a)OR^(9a), —OCX^(a) ₃,—OCHX^(a) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R³ isindependently hydrogen, oxo,halogen, —CX^(b) ₃, —CN, —SO₂Cl, —SO_(n2)R^(10b), SO_(v2)NR^(7b)R^(8b),—NHNH₂, —ONR^(7b)R^(8b), —NHC═(O)NHNH₂,—NHC═(O)NR^(7b)R^(8b), —N(O)_(m2), —NR^(7b)R^(8b), —C(O)R^(9b),—C(O)—OR^(9b), —C(O)NR^(7b)R^(8b), —OR^(10b), —NR^(7b)SO_(n2)R^(10b),—NR^(7b)C═(O)R^(9b), —NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —OCX^(b) ₃,—OCHX^(b) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁴ andR⁵ are independently hydrogen or unsubstituted C₁-C₆ alkyl; R⁷, R⁸, R⁹,R¹⁰, R^(6a), R^(7a), R^(8a), R^(9a), R^(10a), R^(6b), R^(7b), R^(8b),R^(9b) and R^(10b) are independently hydrogen, halogen, —CF₃, —CN, —OH,—NH₂, —COOH, —CONH₂, —NO₂, —SH, —S₂Cl, —S₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁷ andR⁸ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7b) and R^(8b) substituents bonded to thesame nitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; each occurrence of the symbols n, n1, and n2 isindependently an integer from 0 to 4; each occurrence of the symbols m,m1, m2, v, v1, and v2 is independently an integer from 1 to 2; thesymbol z is an integer from 0 to 2; the symbol z2 is an integer from 1to 4; and each occurrence of the symbols X, X^(a), and X^(b) isindependently a halogen.

In another aspect is provided a pharmaceutical composition including apharmaceutically acceptable excipient and a compound, orpharmaceutically acceptable salt thereof, as described herein (e.g.formula I, formula II, formula III, aspect, embodiment, example, figure,table, or claim).

In an aspect is provided a method of treating a disease in a patient inneed of such treatment, the method including administering atherapeutically effective amount of a compound described herein (e.g.formula I, formula II, formula III, aspect, embodiment, example, figure,table, or claim), or a pharmaceutically acceptable salt thereof, to thepatient, wherein the disease is a neurodegenerative disease,demyelinating disease, cancer, eye disease, fibrotic disease, ordiabetes.

In an aspect is provided a method of modulating the activity of an Ire1protein, the method including contacting the Ire1 protein with aneffective amount of a compound described herein (e.g. formula I, formulaII, formula III, aspect, embodiment, example, figure, table, or claim),or a pharmaceutically acceptable salt thereof.

In another aspect, the present disclosure provides compounds having theformula (A):

(also illustrated in FIG. 7) and pharmaceutically acceptable saltsthereof, wherein R^(1d), R^(2d), R^(3d), R^(4d), R^(5d), R^(6d), R^(7d),R^(8d), R^(9d), and R^(10d), are each independently C₂₋₆ alkyl, C₁₋₆haloalkyl, —C₁₋₄ alkyl-R^(12d), C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl,aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenylgroups are each optionally substituted with one or two R^(11d) groups;each R^(11d) is independently C₁₋₆ alkyl, C₁₋₆ haloalkyl, —C(O)R^(d),—C(O)OR^(d), —C(O)NR^(d) ₂, S(O)₂NR^(d) ₂, or —S(O)₂R^(d); and R^(12d)is —OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), OC(O)OR^(d), OC(O)NR^(d) ₂,—N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl,monocyclic heteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl,wherein the aryl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groupsare each optionally substituted by one, two, or three groups that areeach independently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; andeach R^(d) is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆haloalkyl, C₃₋₈ cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl,heteroaryl, or heteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl,heteroaryl, and heteroarylalkyl are optionally substituted with one,two, three, or four groups that are each independently halogen, cyano,nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl, —OR^(0d), SR^(0d), NR^(0d)2,C(O)R^(0d), C(O)OR^(0d), —C(O)N(R^(0d))2, S(O)2R^(0d), —OC(O)R^(0d),—OC(O)OR^(0d), OC(O)N(R^(0d))2, N(R^(0d))C(O)R^(0d),—N(R^(0d))C(O)OR^(0d), or N(R^(0d))C(O)N(R^(0d))2, wherein each R^(0d)is independently hydrogen or C₁₋₆ alkyl, each R^(d) is independentlyhydrogen, or C₁₋₆ alkyl.

In another aspect, R^(2d) and R^(3d) are together a phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O) R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂, N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; wherein each R^(d)is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆ haloalkyl,C₃₋₈ cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl, heteroaryl, orheteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, andheteroarylalkyl are optionally substituted with one, two, three, or fourgroups that are each independently halogen, cyano, nitro, C₁₋₆ alkyl,C₁₋₆ haloalkyl, —OR^(d), SR, NR^(d) ₂, C(O)R^(0d), C(O)OR^(0d),—C(O)N(R^(0d))2, S(O)2R^(0d), —OC(O)R^(0d), —OC(O)OR^(0d),OC(O)N(R^(0d))2, N(R^(0d))C(O)R^(0d), —N(R^(0d))C(O)OR^(0d), orN(R^(0d))C(O)N(R^(0d))2, wherein each R^(0d) is independently hydrogenor C₁₋₆ alkyl, each R^(d) is independently hydrogen, or C₁₋₆ alkyl.

In yet another aspect, R^(1d) is —OR^(d), —SR^(d), —NR^(d) ₂,—C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂, —N(R^(d))C(O)R^(d),—N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂.

In one aspect, the present disclosure is directed to compositions andmethods for activating IRE1α RNase activity using human and murineIRE1α.

In another aspect, the present disclosure is directed to compositionsand methods for inhibiting human and murine IRE1α RNase activity usingcompounds: GP117 (KIRA2), GP118 (KIRA1), GP146 (KIRA3), GP146 (NMe),GP146(Am), Formula B, Formula (A), compounds shown FIGS. 7 and 8, andother derivative compounds disclosed herein

The present disclosure may also be directed to pharmaceuticalcompositions comprising any of the compounds disclosed herein.

In an additional aspect, the present disclosure provides a compoundhaving Formula (B),

and pharmaceutically acceptable salts thereof.

In still another aspect, the present disclosure provides those compoundsillustrated in FIG. 8, and pharmaceutically acceptable salts thereof.

In another aspect, the present disclosure provides methods for treatingdisorders associated with deregulated UPR signaling comprising providingto a patient in need of such treatment a therapeutically effectiveamount of either (i) any of the compounds disclosed herein, or (ii) apharmaceutical composition comprising any of the compounds disclosedherein and a pharmaceutically acceptable excipient, carrier, or diluent.

In another aspect, the present disclosure provides methods for treatingdisorders associated with deregulated UPR signaling comprising providingto a patient in need of such treatment a therapeutically effectiveamount of either a compound of formula (B), the compound illustrated inFIG. 7 and any described derivatives, and those compounds illustrated inFIG. 8 or any of the described or illustrated derivatives thereof, or(ii) a pharmaceutical composition comprising a compound of formula (B)or any of the derivatives thereof described herein and apharmaceutically acceptable excipient, carrier, or diluent, wherein thecompound of formula (B) is

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Interaction of ATP-competitive inhibitors with the bifunctionalkinase/RNase, IRE1α. (a) Proposed binding modes of type I and type IIkinase inhibitors with the ATP-binding pocket of IRE1 α. Left panelshows the contacts a type I inhibitor, APY29, forms with yeast IRE1α(PDB code 3SDJ)¹⁸ (SEQ ID NO:3). The right panel shows the proposedcontacts a type II inhibitor, GP118, forms with IRE1α based on theco-crystal structure of the same inhibitor bound to Src (PDB code 3EL8)(SEQ ID NO:4) (also see FIG. 15). (b) XBP1 RNA minisubstrate assay usedfor screening IRE1α modulators; the recombinant human IRE1α-IRE1α*-usedin the assay spans residues 469-977, which includes the cytosolic kinaseand RNase domains; cleavage of the 5′FAM-3′BHQ-labeled XBP1minisubstrate by IRE1α* results in FRET-dequenching. (c) Endpointfluorescence of IRE1α* catalyzed cleavage reaction of XBP1 minisubstratein the presence of varying concentrations of inhibitors, or DMSO;STF-083010 is an imine-based compound that covalently inhibits the RNasedomain; relative fluorescence intensity is scalcd to the signal observedwith IRE1α* (1.0), or without IRE1α* (0). (mean±SD, n=3). (d) Structuresof type II kinase inhibitors that inhibit the RNase activity of IRE1α*(GP118/KIRA1, GP117/KIRA2, GP146/KIRA3). Numbering of amino acidresidues from Ire1α in figures uses amino acid numbering of human Ire1α(e.g. including numbering used for human IRE1α (469-977) sequence in SEQID NO:2 as numbered in the Examples section herein).

FIG. 2. APY29 and GP146 (KIRA3) divergently modulate the RNase activityand oligomerization state of IRE1α*. (a) Inhibition of IRE1α*autophosphorylation in vitro by APY29 and GP146; top panels showautoradiograms of autophosphorylation levels under serial two-folddilutions of the respective inhibitors (from 80 μM to 0.0098 μM); thelower panel shows normalized autophosphorylation levels and IC₅₀ valuesfor both compounds. (b) λ-PPase treatment of IRE1α* producesdephosphorylated IRE1α* (dP-IRE1α*); immunoblots using anti-IRE1α andanti-phospho IRE1α antibodies are shown. (c) RNase activities of IRE1α*and dP-IRE1α* under varying [APY29] or [GP146] (KIRA3) per the assay ofFIG. 1b ; EC₅₀ values were determined by fitting normalized fluorescenceintensities (mean±SD, n=3). (d) Urea PAGE of XBP1 mini-substratecleavage by IRE1α* and dP-IRE1α* with and without GP146 (KIRA3) orAPY29. (e) RNase competition assays between APY29 and GP146 (KIRA3); theline marked with circles shows IRE1α* RNAse activity under fixed GP146(KIRA3) and varying [APY29]; the line marked with squares shows IRE1α*RNAse activity under fixed APY29 and varying [GP146] (KIRA3); the linemarked with triangles shows RE RNAse activity under fixed STF-083010 andvarying [APY29](mean±SD, n=3).

FIG. 3. Characterization of GP146's interaction with the ATP-bindingsite of IRE1α. (a) A crystal structure of the kinase domain of humanIRE1α bound to ADP; the native cysteine residues that were monitoredusing the ICAT footprinting method are labeled and shown as thick rodsand the DFG-motif is shown as thin bars; cys715 is part of the hingeregion of IRE1α and its side chain partially occupies the ATP-bindingsite; cys645 is in the activation loop, two residues away from theDFG-motif, cys572 is located on the top of the N-terminal lobe of thecatalytic domain and is distant from the ATP-binding site. (b) Resultsof the ICAT footprinting experiments with IRE1α*; alkylation rates weremeasured in the presence of DMSO (circle), APY29 (square) (20 μM), orGP146 (triangle) (20 μM) (mean±SD, n=3). (c) A molecular model ofGP146's interaction with the ATP-binding site of IRE1α; IRE1α is in theDFG-out inactive conformation; the imidazopyrazine ring of GP146occupies the adenine pocket and the 3-trifluoromethylurea occupies theDFG-out pocket; no favorable poses for GP146 bound to the DFG-inconformation of IRE1α could be determined. (d) Control compounds thatwere generated to test the docked structure of GP146 bound to theDFG-out conformation of IRE1α; GP146(NMe) contains a methyl group thatis predicted to disrupt a critical hydrogen bond to the hinge region ofIRE1α GP146(Am) contains an amide rather than a urea group linkerbetween the naphthyl ring and the trifluormethylpheny group; the amidelinker is predicted to lead to a less favorable interaction with theDFG-out pocket; the IC₅₀s for each compound against IRE1α* is listedbelow their structure.

FIG. 4. APY29 and GP146 differentially affect oligomerization state ofIRE1α*. (a) Left panels shows immunoblots of IRE1α* after treatment withthe crosslinker DSS (250 μM); increasing concentrations of IRE1α* wereincubated with DMSO, APY29 (200 μM), or GP146 (200 μM); the right panelshows quantitation of the ratios of oligomeric to monomeric IRE1α* (b)Model of how type I and type II kinase inhibitors affect the RNaseactivities and oligomeric states of IRE1α* and dP-IRE1α*.

FIG. 5. Chemical-genetic modulation of IRE1α kinase and RNase activityin vivo. (a) Anti-total and anti-phospho IRE1α immunoblots of T-Rex 293cells expressing “holed” IRE1α I642A under Doxycycline (Dox) control;cells were pre-treated for 1 hr with GP146 at indicated concentrations,then induced with Dox (1 μM) for 8 hrs; plots show normalizedphosphorylation levels and ratios of spliced XBP1 mRNA under varying[GP146] (mean±SD,n>=3). (b) EtBr-stained agarose gel of XBP1 cDNAamplicons from the cells described in (a). (c) Competition between the“bumped” kinase inhibitor 1NM-PP1 and GP146 against IRE1α I642A; T-Rex293 cells expressing IRE1α I642A were pre-treated for 1 hr with GP146 (1μM) varying [1NM-PP1] before Dox induction (1 μM) for 8 hrs; histogramsshow ratios of spliced XBP1 mRNA as a function of [GP146] and [1NM-PP1].(d) Model of divergent allosteric modulation of IRE1α RNase by type Iand II kinase inhibitors; when overproduced, IRE1α I642A oligomerizesand trans-autophosphorylates, activating XBP1 mRNA splicing by theRNase; type I inhibitor 1NM-PP1 increases—whereas type II inhibitorGP146 decreases—RNase activity; cartoons are not meant to differentiatebetween the relative orientations of monomer subunits in IRE1α.

FIG. 6. Divergent modulation of endogenous IRE1α RNase activity under ERstress with types I and II kinase inhibitors. (a) EtBr-stained agarosegel of XBP1 complementary DNA (cDNA) amplicons from INS-1 cellspre-treated for 1 hr with GP146 or APY29 at indicated concentrations,followed by thapsigargin (Tg) (6 nM) for 4 hrs; ratios of spliced XBP1(XBP1 S) over (spliced+unspliced (XBP1U)) are plotted (mean±SD, n=3).(b) Anti-total and anti-phospho IRE1α immunoblots using extracts fromINS-1 cells pre-treated for 1 hr with GP146, sunitinib, or STF-083010 atindicated concentrations, followed by Tg (6 nM) for 2 hrs. (c)EtBr-stained agarose gel of XBP1 complementary DNA (cDNA) amplicons fromthe INS-1 cells described in (b). (d) EtBr-stained agarose gel of XBP1complementary DNA (cDNA) amplicons from INS-1 cells pre-treated for 1 hrwith GP146(NMe) at indicated concentrations, followed by thapsigargin(Tg) (6 nM) for 4 hrs. (e) Model of how type I kinase inhibitors(APY29), type II kinase inhibitors (GP146), and RNase inhibtors(STF-083010) modulate the enzymatic activities of WT IRE1α. APY29inhibits IRE1α trans-autophosphorylation but promotes oligomerizationand activates the RNase domain; STF-083010 inhibits the RNase activityof IRE1α but does not affect kinase activity or the overalloligomerization state. GP146 inhibits both the kinase and RNase domainsof IRE1α and stabilizes the monomeric form; cartoons are not meant todifferentiate between the relative orientations of monomer subunits inIRE1α.

FIG. 7 illustrates the compound Formula (A), wherein the R¹, R², R³, R⁴,R⁵, R⁶, R⁷, R⁸, R⁹, and R¹⁰ are each defined herein.

FIG. 8 illustrates analogs of GP146 that demonstrate the ability tomodulate and/or inhibit IRE1α RNase activity.

FIG. 9: ER stress-induced apoptosis can be replicated by simplyoverexpressing IRE1α. (A) Percentage of INS-1 cells staining positivefor Annexin V after being treated with increasing concentrations ofThapsigargin (Tg) for 24, 48 and 72 h. (B) Anti-Procaspase-3 and CleavedCaspase-3 immunoblot of INS-1 cells treated with indicatedconcentrations of Tg for 12, 24 and 48 h; anti-GAPDH immunoblot servesas loading control. (C) Model of ER stress mediated activation of IRE1αleading to ER-localized mRNA endonucleolytic decay, terminal UPRendpoints, and apoptosis. (D) Anti-Phospho-IRE1α and anti-Myc immunoblotof INS-1 stable line expressing transgenic wild-type IRE1α (WT) underincreasing doses of Doxycycline (Dox) for 24 h; anti-GAPDH immunoblotserves as loading control. (E) Ethidium-bromide (EtBr)-stained agarosegel of XBP1 cDNA amplicons after induction by treating INS-1 IRE1 α(WT)-expressing stable cells with increasing concentrations of Dox for24 hours; the cDNA amplicon of unspliced XBP1 mRNA is cleaved by a PstIsite within a 26 nucleotide intron to give 2U and 3U; IRE1α-mediatedcleavage of the intron and re-ligation in vivo removes the PstI site togive the 1S (spliced) amplicon; *is a spliced/unspliced XBP1 hybridamplicon; the ratio of spliced over (spliced+unspliced)amplicons—1S/(1S+2U+3U)—is reported as % XBP1 splicing; threeindependent biological samples were used. (F) Q-PCR for Insulin1 mRNA(normalized to GAPDH) in INS-1 IRE1 α (WT)-expressing stable cellstreated with indicated doses of Dox for 24 h. (G) Percent of INS-1 IRE1α (WT)-expressing stable cells staining positive for Annexin V aftertreatment with increasing doses of Dox for 72 h.

FIG. 10. Chemical-genetic manipulation of IRE1α activity reveals boththe necessity and the sufficiency of the IRE1α RNase domain fortriggering apoptosis. (A) Model of IRE1α (I642G) “holed”-kinase mutantand its activation by the “bumped” kinase inhibitor, 1NMPP1. (B) PercentXBP1 splicing in INS-1 IRE1(1642G) stable transgenic cells treated for24 h with 1 μM 1NM-PP1, 1 μg/mL Dox and 6 nM Tg as indicated. (C)Percent of INS-1 IRE1 (I642G) cells staining positive for Annexin Vafter treatment for 72 h with 1 μM 1NM-PP1, 1 μg/mL Dox and 6 nM Tg asindicated. (D) Percent XBP1 splicing in INS-1 IRE1(I642G) and INS-1 IRE1(I642G/N906A) stable transgenic mutant cells treated for 24 h with1NM-PP1, Dox and Tg as indicated. (E) Percent of INS-1 IRE1(I642G) andINS-1 IRE1(I642G/N906A) cells staining positive for Annexin V aftertreatment for 72 h with 1NM-PP1, Dox and Tg as indicated. (F) Anti-Proand Cleaved Caspase-3 immunoblots of INS-1 IRE1 (I642G) and INS-1IRE1(I642G/N906A) mutant stable cells treated for 72 h with 1NM-PP1, Doxand Tg as indicated.

FIG. 11. Direct inhibition of IRE1α RNase prevents IRE1 dependentER-localized mRNA degradation and ER stress-induced apoptosis. (A) Modelof inhibition of IRE1α RNase activity by STF-083010 (STF). (B) PercentXBP1 splicing in INS-1 IRE1 WT stable cells treated with 5 ng/mL Dox and50 μM STF for indicated times as shown (upper panel). EtBr-stainedagarose gel of XBP1 cDNA amplicons is shown for the same samples above(lower panel). (C) Q-PCR for Insulin1 mRNA (normalized to GAPDH) inINS-1 IRE1 WT stable cells treated Dox and STF for 12, 24, 48 and 72 h.(D) Anti-Phospho-IRE1α and Anti-Total IRE1 α immunoblots of INS-1 IRE1WT stable cells treated for 48 h with 5 ng/mL Dox and 50 μM STF. (E)Anti-Phospho and Total JNK immunoblots of same samples. (F) Anti-ProCaspase and Cleaved Caspase-3 immunoblots of same samples. (G) Percentof INS-1 IRE1 WT stable cells staining positive for Annexin V aftertreatment for 72 h with Dox and STF as indicated. (H) Percent of INS-1cells staining positive for Annexin V after treatment for 72 h withincreasing doses of Tunicamycin (Tm) and 50 μM STF as indicated. (I)Immunofluorescence staining on islets from 10 week old C57BL6 micetreated with 0.5 μg/mL Tm and 50 μM STF for 16 h as indicated;co-stained for DAPI (left column), insulin (second column from left),and TUNEL (third column from left); merged image is also shown. (J)Quantification of TUNEL positive β-cells normalized to DAPI-positivecells in (I).

FIG. 12. a) Percent of INS-1 cells staining positive for Annexin-V 72hrs after treatment of 500 ng/ml Tm+/−GP165. (b) EtBr-stained agarosegel of XBP1 cDNA amplicons from INS-1 cells 8 hrs after treatment of 200ng/ml Tm+/−GP165. XBP1U, unspliced XBP1; XBP1S, spliced XBP1; the lowerpanel shows the ratios of spliced XBP1 (XBP1S) over (spliced+unspliced(XBP1U)). (c) Immunoblots for CASP3 cleavage in INS-1 cells 72 hrs aftertreatment of 500 ng/ml Tm+/−GP165 or 50 μM STF-083010 as positivecontrol. (d) qPCR of insulin mRNA in INS-1 cells 8 hrs after treatmentof 500 ng/ml Tm+/−GP165. (e) A schematic model of how GP165 blocksterminal UPR by inhibiting IRE1α activation under ER stress; as a typeII kinase inhibitor, GP165 binds to the adenosine binding pocket andinhibits both the kinase and RNase domains of IRE1α and stabilizes themonomeric form; similar results are obtained using GP146. GP165 isKIRA6.

FIG. 13. Coomassie blue-stained PAGE of purified IRE1*; M, proteinmarker.

FIG. 14. Structures of several type II kinase inhibitors screenedagainst IRE1α* in the XBP1 RNA minisubstrate assay; the relativeendpoint fluorescence intensities for the IRE1α*-catalyzed cleavagereaction of XBP1 minisubstrate in the presence of varying concentrationsof inhibitors are shown.

FIG. 15. Crystal structure of Src bound to the type II kinase inhibitor,GP118 (PDB code 3EL8); hydrogen bond interactions between Src and GP118are denoted as dotted lines; only the backbone atoms are shown forresidues in the hinge region except for Thr338 (gatekeeper residue); theproposed model of GP118 bound to IRE1α shown in FIG. 1a is based on theSrc-GP118 complex structure.

FIG. 16. GP146 and APY29 modulation of IRE1α*-mediated cleavage of an invitro-transcribed 352 nucleotide, internally α 32P-labeled XBP1 RNA. (a)Urea PAGE analysis of 5 minute cleavage reactions of α 32P-labeled XBP1RNA by IRE1α* in the presence of varying concentrations of GP146. (b)Urea PAGE analysis of 5 minute cleavage reactions of α 32P-labeled XBP1RNA by dP-IRE1α* in the presence of varying concentrations of APY29.

FIG. 17. The EC50 of GP146 for IRE1α* RNase inhibition increases in thepresence of a fixed concentration of APY29; the line marked with circlesshows IRE1α* RNase inhibition by GP146 in the absence of a competitor(APY29); the line marked with squares shows IRE1α* RNase inhibition byGP146 in the presence of APY29 (2 μM).

FIG. 18. Sunitinib inhibits IRE1α* autophosphorylation but activates theRNase domain. (a) Autoradiograms of IRE1α* autophosphorylation levelsunder serial two-fold dilutions of sunitinib (from 80 μM to 0.0098 μM).(b) Urea PAGE analysis of XBP1 minisubstrate cleavage by IRE1α* anddP-IRE1α* with and without sunitinib. (c) Urea PAGE analysis of XBP1minisubstrate cleavage by IRE1α* with fixed GP146 (10 μM) and varyingsunitinib concentrations.

FIG. 19. A molecular model of APY29's interaction with the DFG-inconformation of human IRE1α. IRE1α is in the DFG-in active conformation;the pyrimidine ring of APY29 occupies the adenine pocket and the3-aminopyraozole makes several hydrogen bonds with the kinase hinge; nofavorable poses for APY29 bound to the DFG-out conformation of IRE1αcould be determined.

FIG. 20. GP146 inhibits autophosphorylation and XBP1 mRNA splicing by WTIRE1α in T-REx 293 cells. (a) Anti-total and anti-phospho IRE1αimmunoblots, and EtBr-stained agarose gel of XBP1 cDNA amplicons fromT-REx 293 cells expressing WT IRE1α under Doxycycline (Dox) control;cells were pre-treated for 1 hr with GP146 at indicated concentrations,then induced with Dox (1 μM) for 8 hrs. (b) The plot shows normalizedphosphorylation levels under varying [GP146](mean±SD,n>=3). (c)GP146(NMe) does not inhibit XBP1 splicing in T-REx 293 cells expressingWT IRE1α EtBr-stained agarose gel of XBP1 cDNA amplicons from T-REx 293cells expressing WT IRE1α are shown; cells were pre-treated for 1 hrwith GP146(NMe) at indicated concentrations, then induced with Dox (1μM) for 8 hrs.

FIG. 21. Molecular model of GP146 bound to the ATP-binding site of humanIRE1α^(I642A). IRE1α is in the DFG-out inactive conformation; theimidazopyrazine ring of GP146 occupies the adenine pocket and the3-trifluoromethylurea occupies the DFG-out pocket; the naphthyl ring ofGP146 rotates 180 degrees and is able to access the enlarged hydrophobicpocket next to the gatekeeper residue; no favorable poses for GP146bound to the DFG-in conformation of IRE1α^(II642A) could be determined.

FIG. 22. Forced XBP1 mRNA splicing through conditional overproduction ofIRE1α isogenic T-REx 293 stable cell lines; quantitation of EtBr-stainedagarose gels of XBP1 cDNA amplicons from T-REx 293 cells stablyexpressing either WT-IRE1α or the “holed” IRE1α (1642A) mutant underDoxycycline (Dox) control; cells were induced with Dox (1 μM) for 8 hrs,followed by provision of 1NM-PP1 (5 μM)—or DMSO—for 4 more hours; theratio of spliced XBP1 (XBP1S) over (XBP1S+unspliced amplicons (XBP1U))at the endpoint is plotted in the histograms (mean SD, n>=3).

FIG. 23. Death of pancreatic islet β-cells due to unchecked ER stressand terminal UPR signaling is central to development of types 1 and 2diabetes. Compounds, pharmaceutical compositions, and methods describedherein may modulate the UPR and treat diseases associated with ER stressand the UPR.

FIG. 24. (A) Immunoblots of IRE1α* after treatment with the crosslinkerDSS; increasing concentrations of IRE1α* were incubated with DMSO,APY29, or KIRA3. (B) Model of how type kinase inhibitors can affect theRNase activities and oligomeric states of IRE1α* and dP-IRE1α*.

FIG. 25. Synthetic strategy for generating KIRAs.

FIG. 26. Representative KIRAs synthesized and tested.

FIG. 27. (A) General structure of irreversible KIRAs that target acysteine residue located in the activation loop of IRE1; representativeelectrophiles are shown. (B) A close-up of the ATP-binding site ofIRE1α.

FIG. 28. Increasing magnitude and duration of exposure of cells tomyriad ER stressors causes increasing activation of IRE1α(autophosphorylation, XBP1 mRNA splicing, ER localized decay of Ins1mRNA), and switch-like entry of the stressed into dysfunctional statesculminating in apoptosis (see text for details); (A) Percent Annexin-Vstaining INS-1 cells treated in a time course of increasingconcentrations of Tg. (B) Pro- and cleaved Caspase-3 immunoblot ofTg-treated INS-1 cells. (C) Time of exposure to the agent are directlylinked to the percentage of cells entering apoptosis, as can be definedfor other ER stress inducers such as the glycosylation inhibitor,tunicamycin (Tm) (D) Increasing ER stress causes progressive increasesin endogenous IRE1α phosphorylation. (E) Increasing ER stress causesprogressive increases in endogenous XBP1 mRNA splicing. (F) IncreasingER stress causes progressive depletion through endonucleolytic decay ofthe ER-localized mRNA, Ins1, which encodes proinsulin. (G) Increasing ERstress causes progressive induction of the pro-apoptotic transcriptionfactor, CHOP. (H) Diagram of effects due to increasing exposure to ERstress inducers and increasing severity of ER stress.

FIG. 29. Conditional overexpression (using Dox) of IRE1α in stable INS-1cells mimics a Terminal UPR by forcing IRE1α autophosphorylation, XBP1mRNA splicing, ER localized decay of Ins1 mRNA, decay of miR-17,induction of CHOP, accumulation and cleavage of upstream (Caspase 2) anddownstream (Caspase 3) caspases of the mitochondrial apoptotic pathway,as well as inflammatory (Caspase 1) caspase mediating pyroptosis, andswitch-like entry of cells into programmed cell death. (A)Anti-Phospho-IRE1α and anti-Myc-IRE1α immunoblot of INS-1 IRE1α (WT)cells treated with increasing concentrations of Dox for 24 h. (B)Agarose gel of PstI-digested XBP1 cDNA amplicons from INS-1 IRE1α (WT)cells treated with increasing [Dox] for 24 h. % XBP1 splicing representsthe ratio of spliced over (spliced+unspliced) amplicons—1S/(1S+2U+3U).(C) Model of how severe ER stress causes IRE1α to switche fromhomeostatic to apoptotic outputs. (D) Q-PCR for miR-17 in INS-1 IRE1α(WT) cells treated with increasing [Dox] for 72 h. (E) Q-PCR forInsulin1 (Ins1) and CHOP mRNA in INS-1 IRE1α (WT) cells treated withincreasing [Dox] for 24 h; anti-Proinsulin immunoblot of INS-1 IRE1α(WT) cells treated with increasing [Dox] for 72 h. (F) Immunoblot ofPro- and cleaved Caspase-1, Pro- and cleaved Caspase-2 from INS-1 IRE1α(WT) cells treated with increasing [Dox] for 72 h and immunoblot ofPro-Caspase-3 and cleaved Caspase-3 from INS-1 IRE1α (WT) cells treatedwith increasing [Dox] for 72 h. (G) Percent Annexin-V staining of INS-1IRE1α (WT) cells treated with increasing [Dox] for 72 h; threeindependent biological samples were used for XBP1 splicing, Q-PCR andAnnexin V staining experiments; each data point represents the meanvalue±SD; P-values: *<0.05 and **<0.01, ns=not significant.

FIG. 30. KIRA6 inhibits IRE1α autophosphorylation, breaks oligomers,reduces RNase activity, and protects cells from entry into apoptosis.(A) Structure of KIRA6. (B) RNase activities of IRE1α* under varying[KIRA6]; half-maximum effective concentration (EC₅₀) values weredetermined by fitting normalized fluorescence intensities (mean s.d.,n=3). (C) Inhibition of IRE1α* kinase activity in vitro by KIRA6; IC₅₀values were determined by fitting percent phosphorylation. (D) In vivo,KIRA6 inhibits endogenous IRE1α auto-phosphorylation in a dose-dependentmanner; in contrast the aldehyde-based IRE1α RNase-inhibitor, STF, doesnot inhibit IRE1α auto-phosphorylation, nor does a control compoundKIRA6(in). (E) Immunoblots of IRE1α* (WT) incubated with DMSO or KIRA6(200 μM) followed by treatment with the crosslinker DSS (250 μM);quantification is on the right. (F) Agarose gel of XBP1 cDNA ampliconsfrom INS-1 cells pre-treated with indicated concentrations of KIRA6 forh, followed by 0.5 μg/ml Tm for 8 h. (G) KIRA6 inhibits ER-localizedendonucleolytic decay of Ins1 mRNA at lower doses of the drug thanneeded to inhibit XBP1 mRNA splicing. (H) KIRAs reduce entry of INS1-1cells into apoptosis. (I) Immunofluorescence of islets from 10 wk oldC57BL/6 mice treated with 0.5 μg/mL Tm plus/minus 0.5 M KIRA6 for 16 hr.Co-stained for DAPI, insulin, and TUNEL; Quantification of TUNELpositive β-cells (white arrows) normalized to DAPI-positive cells isshown. (J) KIRA6 cytoprotective effects are dependent on IRE1α becausethey are absent in Ire1α^(−/−) mouse embryonic fibroblasts (MEFs), butstill demonstrable in WT and Xbp1^(−/−) MEFs. (K) Model of how KIRA6prevents the terminal UPR by inhibiting IRE1α.

FIG. 31. KIRA6 inhibits IRE1α* RNAse endonucleolytically cleavespre-miR-17 at sites distinct from those cleaved by DICER but related toXBP1 scission sites (A), KIRA6 prevents cleavage of pre-miR-17 by IREα*in vitro (B) cleavage sites (C) pre-miR-17 (D), rescues mature miR-17levels in vivo (E), reduces caspase 2 accumulation and cleavage (F), andprevents TXNIP protein accumulation in C57BL/6 islets exposed to ERstress inducers (G). Sequence legend (FIG. 31B): SEQ ID NOs:11-15 (inorder top to bottom); (FIG. 31C): SEQ ID NO:16.

FIG. 32. Bumped type I kinase inhibitor, 1NM-PP1, increases oligomericstate of holed IRE1α* (I642G) mutant to promote RNAse activity and celldeath under ER stress. (A) Quantitation of the ratios of oligomeric tomonomeric IRE1α*from immunoblots of increasing concentrations ofrecombinant IRE1α*(WT), IRE1α*(I642G) or IRE1*(I642G) incubated with1NM-PP1, before treatment with the crosslinker disuccinimidyl suberate(DSS) (250 Mm) and quantitation of time course of cleavage reactions ofα³²P-labeled XBP1 RNA or Insulin2 (Ins2) RNA by recombinant IRE1α*(WT),IRE1*(I642G), and IRE1α*(I642G) incubated with 1NM-PP1 (10 μM) from ureaPAGE. (B) Percent XBP1 splicing (24 hr), relative Insulin1 (Ins1) mRNAlevels by Q-PCR (24 hr) and percent Annexin V staining (72 hr) in 1μg/mL Dox treated INS-1 IRE1α (I642G) cells plus/minus 1 M 1NM-PP1 andplus/minus 6 nM Tg; three independent biological samples were used foreach experiment and plotted as mean value±SD; P-values: **<0.01. (C)Model for how IRE1α (I642G) is partially activated by 1NMPP1 to spliceXBP1 mRNA in the absence of ER stress; when driven into an oligomericstate by irremediable ER stress, 1NM-PP1-bound IRE1α (I642G) inducesER-localized mRNA decay and Terminal UPR.

FIG. 33. IRE1α RNAse hyperactivation pushes cells into the Terminal UPR.Compounds, pharmaceutical compositions, and methods described herein maymodulate the terminal UPR.

FIG. 34. Death of pancreatic islet β-cells due to unchecked ER stressand terminal UPR signaling is central to development of types 1 and 2diabetes. Compounds, pharmaceutical compositions, and methods describedherein may modulate the UPR and treat diseases associated with ER stressand the UPR.

FIG. 35. Fibrotic remodeling due to unchecked ER stress is central todevelopment of fibrotic disease such as idiopathic pulmonary fibrosis(IPF). Compounds, pharmaceutical compositions, and methods describedherein may modulate the UPR and treat diseases associated with ER stressand the UPR.

FIG. 36. Inhibiting the Terminal UPR by attenuating IRE1α's RNAse withkinase inhibitors (KIRAs).

FIG. 37. KIRA6 shuts down all critical terminal UPR events in pancreaticislet beta cells experiencing ER stress; inhibition of pro-inflammatorysignaling through TXNIP and Interleukin 1-beta.

FIG. 38. Testing cascade to improve potency, selectivity, and efficacyof IRE1α KIRAs.

FIG. 39: KIRA6 protects viability and preserves function of retinalphotoreceptors during tunicamycin- and mutant rhodopsin-induced stress.(A) Fundus and OCT images of Sprague-Dawley rats injected intravitreallywith tunicamycin+/−10 M KIRA6. (B) Fundus and OCT images of P23H-1 ratsat P40 injected intravitreally with DMSO or 10 M KIRA6. (C) Histologicalsections of retinas from P23H-1 rats at P30 after intravitreal injectionof DMSO or 10 M KIRA6. (D) Quantification of outer nuclear layer (ONL)thickness (n=2) of P23H-1 rats at P30; higher thickness line is KIRA6and lower line is DMSO. (E) Fundus and OCT images of P23H-1 rats at P40after intravitreal injection of DMSO or 10 μM KIRA6. (F) Scotopic seriesof ERG measurements with indicated light intensities (top) and aphotopic single flash ERG measurement (+20 dB) (bottom).

FIG. 40. Survival curves of murine embryonic stem cell (ESC)-derivedmotor neurons. A. Wild-type (WT) Hb9:GFP ESCs were differentiated intoGFP+ motor neurons (MNs) and subsequently treated with brefeldin A (BFA)with or without KIRA6 at the indicated concentrations. B.G93A-SOD1/Hb9:GFP ESCs were differentiated into GFP+ MNs and treatedwith KIRA6 at the indicated concentrations; MNs derived from WT Hb9:GFPESCs served as a control. p-values: *<0.05. MutSOD1 leads to a form offamilial amyotrophic lateral sclerosis.

DETAILED DESCRIPTION

Activation of IRE1α's RNase is normally dependent on kinaseautophosphorylation (Tirasophon, W. et al. Genes Dev 12, 1812-1824(1998)), but an allosteric relationship between these two domainsexists, which allows nucleotides (ADP and ATP) and small moleculeinhibitors that stabilize an active ATP-binding site conformation todirectly activate the RNase without autophosphorylation (Papa, F. R. etal. Science 302, 1533-1537 (2003); Han, D. et al. Biochemical andbiophysical research communications 365, 777-783, (2008); Korennykh, A.V. et al. BMC biology 9, 48, (2011)). Furthermore, a particular class ofkinase inhibitors (called type II) stabilize an inactive ATP-bindingsite conformation of IRE1α and are able to potently inhibit its RNaseactivity by breaking high-order oligomerization state (FIGS. 1A and 36)(Wang, L. et al. Nature chemical biology 8, 982-989, (2012)). Thesecompounds are herein labeled—KIRAs—for kinase-inhibitingRNase-attenuators.

Distinct classes of ATP-competitive kinase inhibitors divergentlymodulate the RNase activity of IRE1α. A co-crystal structure of yeastIRE1 bound with APY29—a predicted type I kinase inhibitor—shows that thekinase catalytic domain is in an active conformation, which is aconformation typically adopted by protein kinases when bound to ATP andother type I inhibitors (FIG. 1a ) (Korennykh, A. V. et al. Nature 457,687-693 (2009); Korennykh, A. V. et al. BMC Biol. 9, 48 (2011)).Moreover, two additional co-crystal structures of yeast IRE1 and humanIRE1α bound with ADP show that the kinase domain is similarly in anactive conformation (Ali, M. M. et al. EMBO J. 30, 894-905 (2011); Lee,K. P. et al. Cell 132, 89-100 (2008)). By stabilizing IRE1α's kinase inthe active conformation, these type I inhibitors act as ligands thatallosterically activate its adjacent RNase domain. It might be possibleto stabilize IRE1α's kinase domain in an alternative conformation, andin so doing disable its RNase activity. Use of a class of small moleculekinase inhibitors that have been described to selectively stabilize theinactive conformation of the ATP-binding site (type II inhibitors) for avariety of kinases; examples include the clinically-approved drugsimatinib and sorafenib (Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2,358-364 (2006); Wan, P. T. et al. Cell 116, 855-867 (2004); Schindler,T. et al. Science 289, 1938-1942 (2000)), provides support for thisapproach. The inactive ATP-binding site conformation stabilized by typeII inhibitors is characterized by outward movement of thecatalytically-important Asp-Phe-Gly (DFG) motif, and is therefore calledthe DFG-out conformation (FIG. 1a ) (Liu, Y. & Gray, N. S. Nat. Chem.Biol. 2, 358-364 (2006); Ranjitkar, P. et al. Chem. Biol. 17, 195-206(2010)). In contrast, in all three co-crystal structures of IRE1 in anactive conformation mentioned previously, the kinase domain adopts theDFG-in conformation (Korennykh, A. V. et al. Nature 457, 687-693 (2009);Ali, M. M. et al. EMBO J. 30, 894-905 (2011); Lee, K. P. et al. Cell132, 89-100 (2008)).

Under high endoplasmic reticulum (ER) stress, hyperactivation ofintracellular signaling pathways termed the unfolded protein response(UPR) triggers cell death. Signature events of this “Terminal UPR” arecontrolled by IRE1α, an ER bifunctional kinase/endoribonuclease (RNase),which, when oligomerized, endonucleolytically degrades ER-localizedmRNAs and repressive micro-RNA precursors to trigger apoptosis. Ire1αsomatic mutations found in human cancers disable oligomerization andapoptotic function of its RNase. Using these instructive results fromhuman biology, ATP-competitive kinase inhibitors were developed—termedKRAs (Kinase Inhibiting RNase Attenuators)—that allosterically reduceIRE1α oligomerization and RNase activity. One such kinase inhibitor,KRA6, inhibits all IRE1α outputs, and preserves cell viability andfunction under ER stress. In rat models of retinal degeneration causedby ER stress, intravitreal KIRA6 prevents photoreceptor loss.

A. Definitions

The abbreviations used herein have their conventional meaning within thechemical and biological arts. The chemical structures and formulae setforth herein are constructed according to the standard rules of chemicalvalency known in the chemical arts.

Where substituent groups are specified by their conventional chemicalformulae, written from left to right, they equally encompass thechemically identical substituents that would result from writing thestructure from right to left, e.g., —CH₂O—is equivalent to —OCH₂—. Termsused herein may be preceded and/or followed by a single dash, “ ”, or adouble dash, “=”, to indicate the bond order of the bond between thenamed substituent and its parent moiety; a single dash indicates asingle bond and a double dash indicates a double bond. In the absence ofa single or double dash it is understood that a single bond is formedbetween the substituent and its parent moiety; further, substituentshaving a superscript “d” (e.g. R^(d)) are intended to be read “left toright” unless a dash indicates otherwise. For example, C₁C₆alkoxycarbonyloxy and OC(O)C₁ C₆alkyl indicate the same functionality;similarly arylalkyl and -alkylaryl indicate the same functionality.

The term “saturated” as used herein means the referenced chemicalstructure does not contain any multiple carbon carbon bonds. Forexample, a saturated cycloalkyl group as defined herein includescyclohexyl, cyclopropyl, and the like.

The term “alkyl,” by itself or as part of another substituent, means,unless otherwise stated, a straight (i.e., unbranched) or branchedcarbon chain (or carbon), or combination thereof, which may be fullysaturated, mono- or polyunsaturated and can include di- and multivalentradicals, having the number of carbon atoms designated (i.e., C₁-C₁₀means one to ten carbons). Examples of saturated hydrocarbon radicalsinclude, but are not limited to, groups such as methyl, ethyl, n-propyl,isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl, (cyclohexyl)methyl,homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl,n-octyl, and the like. An unsaturated alkyl group is one having one ormore double bonds or triple bonds. Examples of unsaturated alkyl groupsinclude, but are not limited to, vinyl, 2-propenyl, crotyl,2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl),ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs andisomers. An alkoxy is an alkyl attached to the remainder of the moleculevia an oxygen linker (—O—). In embodiments, an alkyl is a straight orbranched chain hydrocarbon containing from 1 to 10 carbon atoms, unlessotherwise specified. In embodiments, an alkyl is an alkenyl, wherein theterm “alkenyl” is used in accordance with its plain ordinary meaning. Inembodiments, an alkenyl is a straight or branched chain hydrocarboncontaining from 2 to 10 carbons, unless otherwise specified, andcontaining at least one carbon carbon double bond. Examples of alkenylinclude, but are not limited to, ethenyl, 2 propenyl, 2 methyl 2propenyl, 3 butenyl, 4 pentenyl, 5 hexenyl, 2 heptenyl, 2 methyl 1heptenyl, 3 decenyl, and 3,7 dimethylocta 2,6 dienyl. In embodiments, analkyl is an alkynyl, wherein the term “alkynyl” is used in accordancewith its plain ordinary meaning. In embodiments, an alkynyl is astraight or branched chain hydrocarbon group containing from 2 to 10carbon atoms and containing at least one carbon carbon triple bond.Examples of alkynyl include, but are not limited, to acetylenyl, 1propynyl, 2 propynyl, 3 butynyl, 2 pentynyl, and 1 butynyl.

The term “alkylene,” by itself or as part of another substituent, means,unless otherwise stated, a divalent radical derived from an alkyl, asexemplified, but not limited by, —CH₂CH₂CH₂CH₂—. Typically, an alkyl (oralkylene) group will have from 1 to 24 carbon atoms, with those groupshaving 10 or fewer carbon atoms being preferred in the presentinvention. A “lower alkyl” or “lower alkylene” is a shorter chain alkylor alkylene group, generally having eight or fewer carbon atoms. Theterm “alkenylene,” by itself or as part of another substituent, means,unless otherwise stated, a divalent radical derived from an alkene.

The term “heteroalkyl,” by itself or in combination with another term,means, unless otherwise stated, a stable straight or branched chain, orcombinations thereof, including at least one carbon atom and at leastone heteroatom selected from the group consisting of O, N, P, Si, and S,and wherein the nitrogen and sulfur atoms may optionally be oxidized,and the nitrogen heteroatom may optionally be quaternized. Theheteroatom(s) O, N, P, S, and Si may be placed at any interior positionof the heteroalkyl group or at the position at which the alkyl group isattached to the remainder of the molecule. Examples include, but are notlimited to: —CH₂—CH₂—O—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—CH₂—N(CH₃)—CH₃,—CH₂—S—CH₂—CH₃, —CH₂—CH₂—S (O)—CH₃, —CH₂—CH₂—S(O)₂—CH₃, —CH═CHO—CH₃,—Si(CH₃)₃, —CH₂—CH═N—OCH₃, —CH═CH—N(CH₃) —CH₃, —O—CH₃, —O—CH₂—CH₃, and—CN. Up to two or three heteroatoms may be consecutive, such as, forexample, —CH₂—NH—OCH₃ and —CH₂—O—Si(CH₃)₃.

Similarly, the term “heteroalkylene,” by itself or as part of anothersubstituent, means, unless otherwise stated, a divalent radical derivedfrom heteroalkyl, as exemplified, but not limited by,—CH₂—CH₂—S—CH₂—CH₂— and —CH₂—S—CH₂—CH₂—NH—CH₂—. For heteroalkylenegroups, heteroatoms can also occupy either or both of the chain termini(e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, andthe like). Still further, for alkylene and heteroalkylene linkinggroups, no orientation of the linking group is implied by the directionin which the formula of the linking group is written. For example, theformula —C(O)₂R′— represents both —C(O)₂R′— and —R′C(O)₂—. As describedabove, heteroalkyl groups, as used herein, include those groups that areattached to the remainder of the molecule through a heteroatom, such as—C(O)R′, —C(O)NR′, —NR′R″, —OR′, —SR′, and/or —SO₂R′. Where“heteroalkyl” is recited, followed by recitations of specificheteroalkyl groups, such as —NR′R″ or the like, it will be understoodthat the terms heteroalkyl and —NR′R″ are not redundant or mutuallyexclusive. Rather, the specific heteroalkyl groups are recited to addclarity. Thus, the term “heteroalkyl” should not be interpreted hereinas excluding specific heteroalkyl groups, such as —NR′R″ or the like.

The terms “cycloalkyl” and “heterocycloalkyl,” by themselves or incombination with other terms, mean, unless otherwise stated, cyclicversions of “alkyl” and “heteroalkyl,” respectively, wherein the carbonsmaking up the ring or rings do not necessarily need to be bonded to ahydrogen due to all carbon valencies participating in bonds withnon-hydrogen atoms. Additionally, for heterocycloalkyl, a heteroatom canoccupy the position at which the heterocycle is attached to theremainder of the molecule. Examples of cycloalkyl include, but are notlimited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples ofheterocycloalkyl include, but are not limited to,1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl,3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl,1-piperazinyl, 2-piperazinyl, and the like. A “cycloalkylene” and a“heterocycloalkylene,” alone or as part of another substituent, means adivalent radical derived from a cycloalkyl and heterocycloalkyl,respectively.

In embodiments, the term “cycloalkyl” means a monocyclic, bicyclic, or amulticyclic cycloalkyl ring system. In embodiments, monocyclic ringsystems are cyclic hydrocarbon groups containing from 3 to 8 carbonatoms, where such groups can be saturated or unsaturated, but notaromatic. In embodiments, cycloalkyl groups are fully saturated.Examples of monocyclic cycloalkyls include cyclopropyl, cyclobutyl,cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, andcyclooctyl. Bicyclic cycloalkyl ring systems are bridged monocyclicrings or fused bicyclic rings. In embodiments, bridged monocyclic ringscontain a monocyclic cycloalkyl ring where two non adjacent carbon atomsof the monocyclic ring are linked by an alkylene bridge of between oneand three additional carbon atoms (i.e., a bridging group of the form(CH₂)_(w), where w is 1, 2, or 3). Representative examples of bicyclicring systems include, but are not limited to, bicyclo[3.1.1]heptane,bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane,bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane. In embodiments, fusedbicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ringfused to either a phenyl, a monocyclic cycloalkyl, a monocycliccycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. Inembodiments, the bridged or fused bicyclic cycloalkyl is attached to theparent molecular moiety through any carbon atom contained within themonocyclic cycloalkyl ring. In embodiments, cycloalkyl groups areoptionally substituted with one or two groups which are independentlyoxo or thia. In embodiments, the fused bicyclic cycloalkyl is a 5 or 6membered monocyclic cycloalkyl ring fused to either a phenyl ring, a 5or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocycliccycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6membered monocyclic heteroaryl, wherein the fused bicyclic cycloalkyl isoptionally substituted by one or two groups which are independently oxoor thia. In embodiments, multicyclic cycloalkyl ring systems are amonocyclic cycloalkyl ring (base ring) fused to either (i) one ringsystem selected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and abicyclic heterocyclyl; or (ii) two other ring systems independentlyselected from the group consisting of a phenyl, a bicyclic aryl, amonocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl,a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclicheterocyclyl. In embodiments, the multicyclic cycloalkyl is attached tothe parent molecular moiety through any carbon atom contained within thebase ring. In embodiments, multicyclic cycloalkyl ring systems are amonocyclic cycloalkyl ring (base ring) fused to either (i) one ringsystem selected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and abicyclic heterocyclyl; or (ii) two other ring systems independentlyselected from the group consisting of a phenyl, a monocyclic heteroaryl,a monocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclicheterocyclyl. Examples of multicyclic cycloalkyl groups include, but arenot limited to tetradecahydrophenanthrenyl, perhydrophenothiazin-1-yl,and perhydrophenoxazin-1-yl.

In embodiments, a cycloalkyl is a cycloalkenyl. The term “cycloalkenyl”is used in accordance with its plain ordinary meaning. In embodiments, acycloalkenyl is a monocyclic, bicyclic, or a multicyclic cycloalkenylring system. In embodiments, monocyclic cycloalkenyl ring systems arecyclic hydrocarbon groups containing from 3 to 8 carbon atoms, wheresuch groups are unsaturated (i.e., containing at least one annularcarbon carbon double bond), but not aromatic. Examples of monocycliccycloalkenyl ring systems include cyclopentenyl and cyclohexenyl. Inembodiments, bicyclic cycloalkenyl rings are bridged monocyclic rings ora fused bicyclic rings. In embodiments, bridged monocyclic rings containa monocyclic cycloalkenyl ring where two non adjacent carbon atoms ofthe monocyclic ring are linked by an alkylene bridge of between one andthree additional carbon atoms (i.e., a bridging group of the form(CH₂)w, where w is 1, 2, or 3). Representative examples of bicycliccycloalkenyls include, but are not limited to, norbornenyl andbicyclo[2.2.2]oct 2 enyl. In embodiments, fused bicyclic cycloalkenylring systems contain a monocyclic cycloalkenyl ring fused to either aphenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclicheterocyclyl, or a monocyclic heteroaryl. In embodiments, the bridged orfused bicyclic cycloalkenyl is attached to the parent molecular moietythrough any carbon atom contained within the monocyclic cycloalkenylring. In embodiments, cycloalkenyl groups are optionally substitutedwith one or two groups which are independently oxo or thia. Inembodiments, multicyclic cycloalkenyl rings contain a monocycliccycloalkenyl ring (base ring) fused to either (i) one ring systemselected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and abicyclic heterocyclyl; or (ii) two ring systems independently selectedfrom the group consisting of a phenyl, a bicyclic aryl, a monocyclic orbicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl, a monocyclicor bicyclic cycloalkenyl, and a monocyclic or bicyclic heterocyclyl. Inembodiments, the multicyclic cycloalkenyl is attached to the parentmolecular moiety through any carbon atom contained within the base ring.In embodiments, multicyclic cycloalkenyl rings contain a monocycliccycloalkenyl ring (base ring) fused to either (i) one ring systemselected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and abicyclic heterocyclyl; or (ii) two ring systems independently selectedfrom the group consisting of a phenyl, a monocyclic heteroaryl, amonocyclic cycloalkyl, a monocyclic cycloalkenyl, and a monocyclicheterocyclyl.

In embodiments, a heterocycloalkyl is a heterocyclyl. The term“heterocyclyl” as used herein, means a monocyclic, bicyclic, ormulticyclic heterocycle. The heterocyclyl monocyclic heterocycle is a 3,4, 5, 6 or 7 membered ring containing at least one heteroatomindependently selected from the group consisting of O, N, and S wherethe ring is saturated or unsaturated, but not aromatic. The 3 or 4membered ring contains 1 heteroatom selected from the group consistingof O, N and S. The 5 membered ring can contain zero or one double bondand one, two or three heteroatoms selected from the group consisting ofO, N and S. The 6 or 7 membered ring contains zero, one or two doublebonds and one, two or three heteroatoms selected from the groupconsisting of O, N and S. The heterocyclyl monocyclic heterocycle isconnected to the parent molecular moiety through any carbon atom or anynitrogen atom contained within the heterocyclyl monocyclic heterocycle.Representative examples of heterocyclyl monocyclic heterocycles include,but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl,1,3 dioxanyl, 1,3 dioxolanyl, 1,3 dithiolanyl, 1,3 dithianyl,imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl,isoxazolinyl, isoxazolidinyl, morpholinyl, oxadiazolinyl,oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl,pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl,tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl,thiazolinyl, thiazolidinyl, thiomorpholinyl, 1,1 dioxidothiomorpholinyl(thiomorpholine sulfone), thiopyranyl, and trithianyl. The heterocyclylbicyclic heterocycle is a monocyclic heterocycle fused to either aphenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclicheterocycle, or a monocyclic heteroaryl. The heterocyclyl bicyclicheterocycle is connected to the parent molecular moiety through anycarbon atom or any nitrogen atom contained within the monocyclicheterocycle portion of the bicyclic ring system. Representative examplesof bicyclic heterocyclyls include, but are not limited to, 2,3dihydrobenzofuran 2 yl, 2,3 dihydrobenzofuran 3 yl, indolin 1 yl,indolin 2 yl, indolin 3 yl, 2,3 dihydrobenzothien 2 yl,decahydroquinolinyl, decahydroisoquinolinyl, octahydro 1H indolyl, andoctahydrobenzofuranyl. In embodiments, heterocyclyl groups areoptionally substituted with one or two groups which are independentlyoxo or thia. In certain embodiments, the bicyclic heterocyclyl is a 5 or6 membered monocyclic heterocyclyl ring fused to a phenyl ring, a 5 or 6membered monocyclic cycloalkyl, a 5 or 6 membered monocycliccycloalkenyl, a 5 or 6 membered monocyclic heterocyclyl, or a 5 or 6membered monocyclic heteroaryl, wherein the bicyclic heterocyclyl isoptionally substituted by one or two groups which are independently oxoor thia. Multicyclic heterocyclyl ring systems are a monocyclicheterocyclyl ring (base ring) fused to either (i) one ring systemselected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and abicyclic heterocyclyl; or (ii) two other ring systems independentlyselected from the group consisting of a phenyl, a bicyclic aryl, amonocyclic or bicyclic heteroaryl, a monocyclic or bicyclic cycloalkyl,a monocyclic or bicyclic cycloalkenyl, and a monocyclic or bicyclicheterocyclyl. The multicyclic heterocyclyl is attached to the parentmolecular moiety through any carbon atom or nitrogen atom containedwithin the base ring. In embodiments, multicyclic heterocyclyl ringsystems are a monocyclic heterocyclyl ring (base ring) fused to either(i) one ring system selected from the group consisting of a bicyclicaryl, a bicyclic heteroaryl, a bicyclic cycloalkyl, a bicycliccycloalkenyl, and a bicyclic heterocyclyl; or (ii) two other ringsystems independently selected from the group consisting of a phenyl, amonocyclic heteroaryl, a monocyclic cycloalkyl, a monocycliccycloalkenyl, and a monocyclic heterocyclyl. Examples of multicyclicheterocyclyl groups include, but are not limited to10H-phenothiazin-10-yl, 9,10-dihydroacridin-9-yl,9,10-dihydroacridin-10-yl, 10H-phenoxazin-10-yl,10,11-dihydro-5H-dibenzo[b,f]azepin-5-yl,1,2,3,4-tetrahydropyrido[4,3-g]isoquinolin-2-yl,12H-benzo[b]phenoxazin-12-yl, and dodecahydro-1H-carbazol-9-yl.

The terms “halo” or “halogen,” by themselves or as part of anothersubstituent, mean, unless otherwise stated, a fluorine, chlorine,bromine, or iodine atom. Additionally, terms such as “haloalkyl” aremeant to include monohaloalkyl and polyhaloalkyl. For example, the term“halo(C₁—C₄)alkyl” includes, but is not limited to, fluoromethyl,difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl,3-bromopropyl, and the like.

The term “acyl” means, unless otherwise stated, —C(O)R where R is asubstituted or unsubstituted alkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl.

The term “aryl” means, unless otherwise stated, a polyunsaturated,aromatic, hydrocarbon substituent, which can be a single ring ormultiple rings (preferably from 1 to 3 rings) that are fused together(i.e., a fused ring aryl) or linked covalently. A fused ring aryl refersto multiple rings fused together wherein at least one of the fused ringsis an aryl ring. The term “heteroaryl” refers to aryl groups (or rings)that contain at least one heteroatom such as N, O, or S, wherein thenitrogen and sulfur atoms are optionally oxidized, and the nitrogenatom(s) are optionally quaternized. Thus, the term “heteroaryl” includesfused ring heteroaryl groups (i.e., multiple rings fused togetherwherein at least one of the fused rings is a heteroaromatic ring). A5,6-fused ring heteroarylene refers to two rings fused together, whereinone ring has 5 members and the other ring has 6 members, and wherein atleast one ring is a heteroaryl ring. Likewise, a 6,6-fused ringheteroarylene refers to two rings fused together, wherein one ring has 6members and the other ring has 6 members, and wherein at least one ringis a heteroaryl ring. And a 6,5-fused ring heteroarylene refers to tworings fused together, wherein one ring has 6 members and the other ringhas 5 members, and wherein at least one ring is a heteroaryl ring. Aheteroaryl group can be attached to the remainder of the moleculethrough a carbon or heteroatom. Non-limiting examples of aryl andheteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl,1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl,4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl,5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl,4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl,2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl,5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl,5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and6-quinolyl. Substituents for each of the above noted aryl and heteroarylring systems are selected from the group of acceptable substituentsdescribed below. An “arylene” and a “heteroarylene,” alone or as part ofanother substituent, mean a divalent radical derived from an aryl andheteroaryl, respectively, such as for example a divalent radical ofindoline. Non-limiting examples of heteroaryl groups include pyridinyl,pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl,benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl,indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl,benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl,benzothiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl,imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, furylthienyl,pyridyl, pyrimidyl, benzothiazolyl, purinyl, benzimidazolyl,isoquinolyl, thiadiazolyl, oxadiazolyl, pyrrolyl, diazolyl, triazolyl,tetrazolyl, benzothiadiazolyl, isothiazolyl, pyrazolopyrimidinyl,pyrrolopyrimidinyl, benzotriazolyl, benzoxazolyl, or quinolyl. Theexamples above may be substituted or unsubstituted and divalent radicalsof each heteroaryl example above are non-limiting examples ofheteroarylene.

In embodiments, an aryl is a phenyl (i.e., monocyclic aryl), a bicyclicring system containing at least one phenyl ring or an aromatic bicyclicring containing only carbon atoms in the aromatic bicyclic ring systemor a multicyclic aryl ring system, provided that the bicyclic ormulticyclic aryl ring system does not contain a heteroaryl ring whenfully aromatic. In embodiments, the bicyclic aryl can be azulenyl,naphthyl, or a phenyl fused to a monocyclic cycloalkyl, a monocycliccycloalkenyl, or a monocyclic heterocyclyl. In embodiments, the bicyclicaryl may be attached to the parent molecular moiety through any carbonatom contained within the phenyl portion of the bicyclic system, or anycarbon atom with the napthyl or azulenyl ring. In embodiments, the fusedmonocyclic cycloalkyl or monocyclic heterocyclyl portions of thebicyclic aryl are optionally substituted with one or two oxo and/or thiagroups. Representative examples of the bicyclic aryls include, but arenot limited to, azulenyl, naphthyl, dihydroinden 1 yl, dihydroinden 2yl, dihydroinden 3 yl, dihydroinden 4 yl, 2,3 dihydroindol 4 yl, 2,3dihydroindol 5 yl, 2,3 dihydroindol 6 yl, 2,3 dihydroindol 7 yl, inden 1yl, inden 2 yl, inden 3 yl, inden 4 yl, dihydronaphthalen 2 yl,dihydronaphthalen 3 yl, dihydronaphthalen 4 yl, dihydronaphthalen 1 yl,5,6,7,8 tetrahydronaphthalen 1 yl, 5,6,7,8 tetrahydronaphthalen 2 yl,2,3 dihydrobenzofuran 4 yl, 2,3 dihydrobenzofuran 5 yl, 2,3dihydrobenzofuran 6 yl, 2,3 dihydrobenzofuran 7 yl, benzo[d][1,3]dioxol4 yl, benzo[d][1,3]dioxol 5 yl, 2H chromen 2 on 5 yl, 2H chromen 2 on 6yl, 2H chromen 2 on 7 yl, 2H chromen 2 on 8 yl, isoindoline 1,3 dion 4yl, isoindoline 1,3 dion 5 yl, inden 1 on 4 yl, inden 1 on 5 yl, inden 1on 6 yl, inden 1 on 7 yl, 2,3 dihydrobenzo[b][1,4]dioxan 5 yl, 2,3dihydrobenzo[b][1,4]dioxan 6 yl, 2H benzo[b][1,4]oxazin3(4H) on 5 yl, 2Hbenzo[b][1,4]oxazin3(4H) on 6 yl, 2H benzo[b][1,4]oxazin3(4H) on 7 yl,2H benzo[b][1,4]oxazin3(4H) on 8 yl, benzo[d]oxazin 2(3H) on 5 yl,benzo[d]oxazin 2(3H) on 6 yl, benzo[d]oxazin 2(3H) on 7 yl,benzo[d]oxazin 2(3H) on 8 yl, quinazolin 4(3H) on 5 yl, quinazolin 4(3H)on 6 yl, quinazolin 4(3H) on 7 yl, quinazolin 4(3H) on 8 yl, quinoxalin2(1H) on 5 yl, quinoxalin 2(1H) on 6 yl, quinoxalin 2(1H) on 7 yl,quinoxalin 2(1H) on 8 yl, benzo[d]thiazol 2(3H) on 4 yl, benzo[d]thiazol2(3H) on 5 yl, benzo[d]thiazol 2(3H) on 6 yl, and, benzo[d]thiazol 2(3H)on 7 yl. In embodiments, the bicyclic aryl is (i) naphthyl or (ii) aphenyl ring fused to either a 5 or 6 membered monocyclic cycloalkyl, a 5or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclicheterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, andheterocyclyl groups are optionally substituted with one or two groupswhich are independently oxo or thia. In embodiments, multicyclic arylgroups are a phenyl ring (base ring) fused to either (i) one ring systemselected from the group consisting of a bicyclic aryl, a bicycliccycloalkyl, a bicyclic cycloalkenyl, and a bicyclic heterocyclyl; or(ii) two other ring systems independently selected from the groupconsisting of a phenyl, a bicyclic aryl, a monocyclic or bicycliccycloalkyl, a monocyclic or bicyclic cycloalkenyl, and a monocyclic orbicyclic heterocyclyl, provided that when the base ring is fused to abicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclic heterocyclyl,then the base ring is fused to the base ring of the bicyclic cycloalkyl,bicyclic cycloalkenyl, or bicyclic heterocyclyl. In embodiments, themulticyclic aryl may be attached to the parent molecular moiety throughany carbon atom contained within the base ring. In certain embodiments,multicyclic aryl groups are a phenyl ring (base ring) fused to either(i) one ring system selected from the group consisting of a bicyclicaryl, a bicyclic cycloalkyl, a bicyclic cycloalkenyl, and a bicyclicheterocyclyl; or (ii) two other ring systems independently selected fromthe group consisting of a phenyl, a monocyclic cycloalkyl, a monocycliccycloalkenyl, and a monocyclic heterocyclyl, provided that when the basering is fused to a bicyclic cycloalkyl, bicyclic cycloalkenyl, orbicyclic heterocyclyl, then the base ring is fused to the base ring ofthe bicyclic cycloalkyl, bicyclic cycloalkenyl, or bicyclicheterocyclyl. Examples of multicyclic aryl groups include but are notlimited to anthracen-9-yl and phenanthren-9-yl.

In embodiments, the term “heteroaryl,” as used herein, means amonocyclic, bicyclic, or a multicyclic heteroaryl ring system. Inembodiments, the monocyclic heteroaryl can be a 5 or 6 membered ring. Inembodiments, the 5 membered ring consists of two double bonds and one,two, three or four nitrogen atoms and optionally one oxygen or sulfuratom. In embodiments, the 6 membered ring consists of three double bondsand one, two, three or four nitrogen atoms. In embodiments, the 5 or 6membered heteroaryl is connected to the parent molecular moiety throughany carbon atom or any nitrogen atom contained within the heteroaryl.Representative examples of monocyclic heteroaryl include, but are notlimited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl,oxazolyl, pyridinyl, pyridazinyl, pyrimidinyl, pyrazinyl, pyrazolyl,pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, andtriazinyl. In embodiments, the bicyclic heteroaryl consists of amonocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, amonocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclicheteroaryl. In embodiments, the fused cycloalkyl or heterocyclyl portionof the bicyclic heteroaryl group is optionally substituted with one ortwo groups which are independently oxo or thia. In embodiments, when thebicyclic heteroaryl contains a fused cycloalkyl, cycloalkenyl, orheterocyclyl ring, then the bicyclic heteroaryl group is connected tothe parent molecular moiety through any carbon or nitrogen atomcontained within the monocyclic heteroaryl portion of the bicyclic ringsystem. In embodiments, when the bicyclic heteroaryl is a monocyclicheteroaryl fused to a phenyl ring or a monocyclic heteroaryl, then thebicyclic heteroaryl group is connected to the parent molecular moietythrough any carbon atom or nitrogen atom within the bicyclic ringsystem. Representative examples of bicyclic heteroaryl include, but arenot limited to, benzimidazolyl, benzofuranyl, benzothienyl,benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5,6dihydroquinolin 2 yl, 5,6 dihydroisoquinolin 1 yl, furopyridinyl,indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl,5,6,7,8 tetrahydroquinolin 2 yl, 5,6,7,8 tetrahydroquinolin 3 yl,5,6,7,8 tetrahydroquinolin 4 yl, 5,6,7,8 tetrahydroisoquinolin 1 yl,thienopyridinyl, 4,5,6,7 tetrahydrobenzo[c][1,2,5]oxadiazolyl, and 6,7dihydrobenzo[c][1,2,5]oxadiazol 4(5H) onyl. In embodiments, the fusedbicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ringfused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl,a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclicheterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein thefused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionallysubstituted with one or two groups which are independently oxo or thia.In embodiments, the multicyclic heteroaryl group is a monocyclicheteroaryl ring (base ring) fused to either (i) one ring system selectedfrom the group consisting of a bicyclic aryl, a bicyclic heteroaryl, abicyclic heterocyclyl, a bicyclic cycloalkenyl, and a bicycliccycloalkyl; or (ii) two ring systems selected from the group consistingof a phenyl, a bicyclic aryl, a monocyclic or bicyclic heteroaryl, amonocyclic or bicyclic heterocyclyl, a monocyclic or bicycliccycloalkenyl, and a monocyclic or bicyclic cycloalkyl. In embodiments,the multicyclic heteroaryl group is connected to the parent molecularmoiety through any carbon atom or nitrogen atom contained within thebase ring. In embodiments, multicyclic heteroaryl groups are amonocyclic heteroaryl ring (base ring) fused to either (i) one ringsystem selected from the group consisting of a bicyclic aryl, a bicyclicheteroaryl, a bicyclic heterocyclyl, a bicyclic cycloalkenyl, and abicyclic cycloalkyl; or (ii) two ring systems selected from the groupconsisting of a phenyl, a monocyclic heteroaryl, a monocyclicheterocyclyl, a monocyclic cycloalkenyl, and a monocyclic cycloalkyl.Examples of multicyclic heteroaryls include, but are not limited to5H-[1,2,4]triazino[5,6-b]indol-5-yl,2,3,4,9-tetrahydro-1H-carbazol-9-yl, 9H-pyrido[3,4-b]indol-9-yl,9H-carbazol-9-yl, acridin-9-yl,

A fused ring heterocyloalkyl-aryl is an aryl fused to aheterocycloalkyl. A fused ring heterocycloalkyl-heteroaryl is aheteroaryl fused to a heterocycloalkyl. A fused ringheterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a cycloalkyl.A fused ring heterocycloalkyl-heterocycloalkyl is a heterocycloalkylfused to another heterocycloalkyl. Fused ring heterocycloalkyl-aryl,fused ring heterocycloalkyl-heteroaryl, fused ringheterocycloalkyl-cycloalkyl, or fused ringheterocycloalkyl-heterocycloalkyl may each independently beunsubstituted or substituted with one or more of the substitutentsdescribed herein.

The term “oxo,” as used herein, means an oxygen that is double bonded toa carbon atom. The term “thia” as used herein means a=S group.

The term “alkylsulfonyl,” as used herein, means a moiety having theformula —S(O)₂—R′, where R′ is a substituted or unsubstituted alkylgroup as defined above. R′ may have a specified number of carbons (e.g.,“C₁-C₄ alkylsulfonyl”).

The term “arylalkyl” and “alkylaryl” as used herein, means an arylgroup, as defined herein, appended to the parent molecular moietythrough an alkyl group, as defined herein. Representative examples ofarylalkyl include, but are not limited to, benzyl, 2 phenylethyl, 3phenylpropyl, and 2 naphth 2 ylethyl.

The term “heteroarylalkyl” and “alkylheteroaryl” as used herein, means aheteroaryl, as defined herein, appended to the parent molecular moietythrough an alkyl group, as defined herein. Representative examples ofheteroarylalkyl include, but are not limited to, fur 3 ylmethyl, 1Himidazol 2 ylmethyl, 1H imidazol 4 ylmethyl, 1 (pyridin 4 yl)ethyl,pyridin 3 ylmethyl, pyridin 4 ylmethyl, pyrimidin 5 ylmethyl, 2(pyrimidin 2 yl)propyl, thien 2 ylmethyl, and thien 3 ylmethyl.

Each of the above terms (e.g., “alkyl,” “heteroalkyl,” “aryl,” and“heteroaryl”) includes both substituted and unsubstituted forms of theindicated radical. Preferred substituents for each type of radical areprovided below.

Substituents for the alkyl and heteroalkyl radicals (including thosegroups often referred to as alkylene, alkenyl, heteroalkylene,heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, andheterocycloalkenyl) can be one or more of a variety of groups selectedfrom, but not limited to, —OR′, ═O, ═NR′, ═N—OR′, —NR′R″, —SR′,-halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″,—NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″,—NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —NR′NR″R′″,—ONR′R″, —NR′C═(O)NR″NR′″R″″, —CN, —NO₂, in a number ranging from zeroto (2m′+1), where m′ is the total number of carbon atoms in suchradical. R, R′, R″, R′″, and R″″ each preferably independently refer tohydrogen, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl (e.g., aryl substituted with 1-3halogens), substituted or unsubstituted heteroaryl, substituted orunsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups.When a compound of the invention includes more than one R group, forexample, each of the R groups is independently selected as are each R′,R″, R′″, and R″″ group when more than one of these groups is present.When R′ and R″ are attached to the same nitrogen atom, they can becombined with the nitrogen atom to form a 4-, 5-, 6-, or 7-memberedring. For example, —NR′R″ includes, but is not limited to,1-pyrrolidinyl and 4-morpholinyl. From the above discussion ofsubstituents, one of skill in the art will understand that the term“alkyl” is meant to include groups including carbon atoms bound togroups other than hydrogen groups, such as haloalkyl (e.g., —CF₃ and—CH₂CF₃) and acyl (e.g., —C(O)CH₃, —C(O)CF₃, —C(O)CH₂OCH₃, and thelike).

Similar to the substituents described for the alkyl radical,substituents for the aryl and heteroaryl groups are varied and areselected from, for example: —OR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″,—OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O) NR′R″, —NR″C(O)R′,—NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″, —NR—C(NR′R″)═N R′″,—S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —NR′NR″R′″, —ONR′R″,—NR′C═(O)NR″NR′″R″″, —CN, —NO₂, —R′, —N₃, —CH(Ph)₂, fluoro(C₁-C₄)alkoxy,and fluoro(C₁-C₄)alkyl, in a number ranging from zero to the totalnumber of open valences on the aromatic ring system; and where R′, R″,R′″, and R″″ are preferably independently selected from hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, andsubstituted or unsubstituted heteroaryl. When a compound of theinvention includes more than one R group, for example, each of the Rgroups is independently selected as are each R′, R″, R′″, and R″″ groupswhen more than one of these groups is present.

Two or more substituents may optionally be joined to form aryl,heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such so-calledring-forming substituents are typically, though not necessarily, foundattached to a cyclic base structure. In one embodiment, the ring-formingsubstituents are attached to adjacent members of the base structure. Forexample, two ring-forming substituents attached to adjacent members of acyclic base structure create a fused ring structure. In anotherembodiment, the ring-forming substituents are attached to a singlemember of the base structure. For example, two ring-forming substituentsattached to a single member of a cyclic base structure create aspirocyclic structure. In yet another embodiment, the ring-formingsubstituents are attached to non-adjacent members of the base structure.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ringmay optionally form a ring of the formula -T-C(O)—(CRR′)_(q)—U—, whereinT and U are independently —NR—, —O—, —CRR′—, or a single bond, and q isan integer of from 0 to 3. Alternatively, two of the substituents onadjacent atoms of the aryl or heteroaryl ring may optionally be replacedwith a substituent of the formula -A-(CH₂)_(r)—B—, wherein A and B areindependently —CRR′—, —O—, —NR—, —S—, —S(O)—, —S(O)₂—, —S(O)₂NR′—, or asingle bond, and r is an integer of from 1 to 4. One of the single bondsof the new ring so formed may optionally be replaced with a double bond.Alternatively, two of the substituents on adjacent atoms of the aryl orheteroaryl ring may optionally be replaced with a substituent of theformula —(CRR′)_(s)—X′—(C″R″R′″)_(d)—, where s and d are independentlyintegers of from 0 to 3, and X′ is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or—S(O)₂NR′—. The substituents R, R′, R″, and R′″ are preferablyindependently selected from hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, and substituted or unsubstitutedheteroaryl.

As used herein, the terms “heteroatom” or “ring heteroatom” are meant toinclude, oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), andsilicon (Si).

A “substituent group,” as used herein, means a group selected from thefollowing moieties:

(A) oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,—SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, —NHSO₂CH₃,—N₃, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstitutedcycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl,unsubstituted heteroaryl, and(B) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl,substituted with at least one substituent selected from:

-   -   (i) oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂,        —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,        —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH,        —NHOH, —OCF₃, —OCHF₂, —NHSO₂CH₃, —N₃, unsubstituted alkyl,        unsubstituted heteroalkyl, unsubstituted cycloalkyl,        unsubstituted heterocycloalkyl, unsubstituted aryl,        unsubstituted heteroaryl, and    -   (ii) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl,        heteroaryl, substituted with at least one substituent selected        from:        -   (a) oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂,            —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,            —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH,            —NHOH, —OCF₃, —OCHF₂, —NHSO₂CH₃, —N₃, unsubstituted alkyl,            unsubstituted heteroalkyl, unsubstituted cycloalkyl,            unsubstituted heterocycloalkyl, unsubstituted aryl,            unsubstituted heteroaryl, and        -   (b) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl,            heteroaryl, substituted with at least one substituent            selected from: oxo,        -   halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,            —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,            —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃,            —OCHF₂, —NHSO₂CH₃, —N₃, unsubstituted alkyl, unsubstituted            heteroalkyl, unsubstituted cycloalkyl, unsubstituted            heterocycloalkyl, unsubstituted aryl, unsubstituted            heteroaryl.

A “size-limited substituent” or “size-limited substituent group,” asused herein, means a group selected from all of the substituentsdescribed above for a “substituent group,” wherein each substituted orunsubstituted alkyl is a substituted or unsubstituted C₁-C₂₀ alkyl, eachsubstituted or unsubstituted heteroalkyl is a substituted orunsubstituted 2 to 20 membered heteroalkyl, each substituted orunsubstituted cycloalkyl is a substituted or unsubstituted C₃-C₈cycloalkyl, each substituted or unsubstituted heterocycloalkyl is asubstituted or unsubstituted 3 to 8 membered heterocycloalkyl, eachsubstituted or unsubstituted aryl is a substituted or unsubstitutedC₆-C₁₀ aryl, and each substituted or unsubstituted heteroaryl is asubstituted or unsubstituted 5 to 10 membered heteroaryl.

A “lower substituent” or “lower substituent group,” as used herein,means a group selected from all of the substituents described above fora “substituent group,” wherein each substituted or unsubstituted alkylis a substituted or unsubstituted C₁-C₈ alkyl, each substituted orunsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₇ cycloalkyl, each substituted orunsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7membered heterocycloalkyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 9membered heteroaryl.

In some embodiments, each substituted group described in the compoundsherein is substituted with at least one substituent group. Morespecifically, in some embodiments, each substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, substituted heteroaryl, substituted alkylene,substituted heteroalkylene, substituted cycloalkylene, substitutedheterocycloalkylene, substituted arylene, and/or substitutedheteroarylene described in the compounds herein are substituted with atleast one substituent group. In other embodiments, at least one or allof these groups are substituted with at least one size-limitedsubstituent group. In other embodiments, at least one or all of thesegroups are substituted with at least one lower substituent group.

In other embodiments of the compounds herein, each substituted orunsubstituted alkyl may be a substituted or unsubstituted C₁-C₂₀ alkyl,each substituted or unsubstituted heteroalkyl is a substituted orunsubstituted 2 to 20 membered heteroalkyl, each substituted orunsubstituted cycloalkyl is a substituted or unsubstituted C₃-C₈cycloalkyl, each substituted or unsubstituted heterocycloalkyl is asubstituted or unsubstituted 3 to 8 membered heterocycloalkyl, eachsubstituted or unsubstituted aryl is a substituted or unsubstitutedC₆-C₁₀ aryl, and/or each substituted or unsubstituted heteroaryl is asubstituted or unsubstituted 5 to 10 membered heteroaryl. In someembodiments of the compounds herein, each substituted or unsubstitutedalkylene is a substituted or unsubstituted C₁-C₂₀ alkylene, eachsubstituted or unsubstituted heteroalkylene is a substituted orunsubstituted 2 to 20 membered heteroalkylene, each substituted orunsubstituted cycloalkylene is a substituted or unsubstituted C₃-C₈cycloalkylene, each substituted or unsubstituted heterocycloalkylene isa substituted or unsubstituted 3 to 8 membered heterocycloalkylene, eachsubstituted or unsubstituted arylene is a substituted or unsubstitutedC₆-C₁₀ arylene, and/or each substituted or unsubstituted heteroaryleneis a substituted or unsubstituted 5 to 10 membered heteroarylene.

In some embodiments, each substituted or unsubstituted alkyl is asubstituted or unsubstituted C₁-C₈ alkyl, each substituted orunsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₇ cycloalkyl, each substituted orunsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7membered heterocycloalkyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and/or each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 9membered heteroaryl. In some embodiments, each substituted orunsubstituted alkylene is a substituted or unsubstituted C₁-C₈ alkylene,each substituted or unsubstituted heteroalkylene is a substituted orunsubstituted 2 to 8 membered heteroalkylene, each substituted orunsubstituted cycloalkylene is a substituted or unsubstituted C₃-C₇cycloalkylene, each substituted or unsubstituted heterocycloalkylene isa substituted or unsubstituted 3 to 7 membered heterocycloalkylene, eachsubstituted or unsubstituted arylene is a substituted or unsubstitutedC₆-C₁₀ arylene, and/or each substituted or unsubstituted heteroaryleneis a substituted or unsubstituted 5 to 9 membered heteroarylene. In someembodiments, the compound is a chemical species set forth in theExamples section below.

The term “pharmaceutically acceptable salts” is meant to include saltsof the active compounds that are prepared with relatively nontoxic acidsor bases, depending on the particular substituents found on thecompounds described herein. When compounds of the present inventioncontain relatively acidic functionalities, base addition salts can beobtained by contacting the neutral form of such compounds with asufficient amount of the desired base, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable base additionsalts include sodium, potassium, calcium, ammonium, organic amino, ormagnesium salt, or a similar salt. When compounds of the presentinvention contain relatively basic functionalities, acid addition saltscan be obtained by contacting the neutral form of such compounds with asufficient amount of the desired acid, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable acid additionsalts include those derived from inorganic acids like hydrochloric,hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,monohydrogensulfuric, hydriodic, or phosphorous acids and the like, aswell as the salts derived from relatively nontoxic organic acids likeacetic, propionic, isobutyric, maleic, malonic, benzoic, succinic,suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic,p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Alsoincluded are salts of amino acids such as arginate and the like, andsalts of organic acids like glucuronic or galactunoric acids and thelike (see, e.g., Berge et al., Journal of Pharmaceutical Science 66:1-19(1977)). Certain specific compounds of the present invention containboth basic and acidic functionalities that allow the compounds to beconverted into either base or acid addition salts. Otherpharmaceutically acceptable carriers known to those of skill in the artare suitable for the present invention. Salts tend to be more soluble inaqueous or other protonic solvents that are the corresponding free baseforms. In other cases, the preparation may be a lyophilized powder in 1mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5to 5.5, that is combined with buffer prior to use.

Thus, the compounds of the present invention may exist as salts, such aswith pharmaceutically acceptable acids. The present invention includessuch salts. Examples of such salts include hydrochlorides,hydrobromides, sulfates, methanesulfonates, nitrates, maleates,acetates, citrates, fumarates, tartrates (e.g., (+)-tartrates,(−)-tartrates, or mixtures thereof including racemic mixtures),succinates, benzoates, and salts with amino acids such as glutamic acid.These salts may be prepared by methods known to those skilled in theart.

The neutral forms of the compounds are preferably regenerated bycontacting the salt with a base or acid and isolating the parentcompound in the conventional manner. The parent form of the compounddiffers from the various salt forms in certain physical properties, suchas solubility in polar solvents.

In addition to salt forms, the present invention provides compounds,which are in a prodrug form. Prodrugs of the compounds described hereinare those compounds that readily undergo chemical changes underphysiological conditions to provide the compounds of the presentinvention. Additionally, prodrugs can be converted to the compounds ofthe present invention by chemical or biochemical methods in an ex vivoenvironment. For example, prodrugs can be slowly converted to thecompounds of the present invention when placed in a transdermal patchreservoir with a suitable enzyme or chemical reagent.

Certain compounds of the present invention can exist in unsolvated formsas well as solvated forms, including hydrated forms. In general, thesolvated forms are equivalent to unsolvated forms and are encompassedwithin the scope of the present invention. Certain compounds of thepresent invention may exist in multiple crystalline or amorphous forms.In general, all physical forms are equivalent for the uses contemplatedby the present invention and are intended to be within the scope of thepresent invention.

As used herein, the term “salt” refers to acid or base salts of thecompounds used in the methods of the present invention. Illustrativeexamples of acceptable salts are mineral acid (hydrochloric acid,hydrobromic acid, phosphoric acid, and the like) salts, organic acid(acetic acid, propionic acid, glutamic acid, citric acid and the like)salts, quaternary ammonium (methyl iodide, ethyl iodide, and the like)salts.

Certain compounds of the present invention possess asymmetric carbonatoms (optical or chiral centers) or double bonds; the enantiomers,racemates, diastereomers, tautomers, geometric isomers, stereoisometricforms that may be defined, in terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or (L)- for amino acids, and individual isomers areencompassed within the scope of the present invention. The compounds ofthe present invention do not include those which are known in art to betoo unstable to synthesize and/or isolate. The present invention ismeant to include compounds in racemic and optically pure forms.Optically active (R)- and (S)-, or (D)- and (L)-isomers may be preparedusing chiral synthons or chiral reagents, or resolved using conventionaltechniques. When the compounds described herein contain olefinic bondsor other centers of geometric asymmetry, and unless specified otherwise,it is intended that the compounds include both E and Z geometricisomers.

As used herein, the term “isomers” refers to compounds having the samenumber and kind of atoms, and hence the same molecular weight, butdiffering in respect to the structural arrangement or configuration ofthe atoms.

The term “tautomer,” as used herein, refers to one of two or morestructural isomers which exist in equilibrium and which are readilyconverted from one isomeric form to another.

It will be apparent to one skilled in the art that certain compounds ofthis invention may exist in tautomeric forms, all such tautomeric formsof the compounds being within the scope of the invention.

Unless otherwise stated, structures depicted herein are also meant toinclude all stereochemical forms of the structure; i.e., the R and Sconfigurations for each asymmetric center. Therefore, singlestereochemical isomers as well as enantiomeric and diastereomericmixtures of the present compounds are within the scope of the invention.

Unless otherwise stated, structures depicted herein are also meant toinclude compounds which differ only in the presence of one or moreisotopically enriched atoms. For example, compounds having the presentstructures except for the replacement of a hydrogen by a deuterium ortritium, or the replacement of a carbon by ¹³C- or ¹⁴C-enriched carbonare within the scope of this invention.

The compounds of the present invention may also contain unnaturalproportions of atomic isotopes at one or more of the atoms thatconstitute such compounds. For example, the compounds may beradiolabeled with radioactive isotopes, such as for example tritium(³H), iodine-125 (¹²⁵I), or carbon-14 (¹⁴C). All isotopic variations ofthe compounds of the present invention, whether radioactive or not, areencompassed within the scope of the present invention.

The symbol “

” denotes the point of attachment of a chemical moiety to the remainderof a molecule or chemical formula.

The terms “a” or “an,” as used in herein means one or more. In addition,the phrase “substituted with a[n],” as used herein, means the specifiedgroup may be substituted with one or more of any or all of the namedsubstituents. For example, where a group, such as an alkyl or heteroarylgroup, is “substituted with an unsubstituted C₁-C₂₀ alkyl, orunsubstituted 2 to 20 membered heteroalkyl,” the group may contain oneor more unsubstituted C₁-C₂₀ alkyls, and/or one or more unsubstituted 2to 20 membered heteroalkyls. Moreover, where a moiety is substitutedwith an R substituent, the group may be referred to as “R-substituted.”Where a moiety is R-substituted, the moiety is substituted with at leastone R substituent and each R substituent is optionally different.

Descriptions of compounds of the present invention are limited byprinciples of chemical bonding known to those skilled in the art.Accordingly, where a group may be substituted by one or more of a numberof substituents, such substitutions are selected so as to comply withprinciples of chemical bonding and to give compounds which are notinherently unstable and/or would be known to one of ordinary skill inthe art as likely to be unstable under ambient conditions, such asaqueous, neutral, and several known physiological conditions. Forexample, a heterocycloalkyl or heteroaryl is attached to the remainderof the molecule via a ring heteroatom in compliance with principles ofchemical bonding known to those skilled in the art thereby avoidinginherently unstable compounds.

The terms “treating” or “treatment” refers to any indicia of success inthe treatment or amelioration of an injury, disease, pathology orcondition, including any objective or subjective parameter such asabatement; remission; diminishing of symptoms or making the injury,pathology or condition more tolerable to the patient; slowing in therate of degeneration or decline; making the final point of degenerationless debilitating; improving a patient's physical or mental well-being.The treatment or amelioration of symptoms can be based on objective orsubjective parameters; including the results of a physical examination,neuropsychiatric exams, and/or a psychiatric evaluation. For example,certain methods herein treat cancer (e.g. multiple myeloma, cancers ofsecretory cells), neurodegenerative diseases, demyelinating diseases,eye diseases, fibrotic diseases, or diabetes (type I or type II). Forexample certain methods herein treat cancer by decreasing or reducing orpreventing the occurrence, growth, metastasis, or progression of cancer;treat neurodegeneration by improving mental wellbeing, increasing mentalfunction, slowing the decrease of mental function, decreasing dementia,delaying the onset of dementia, improving cognitive skills, decreasingthe loss of cognitive skills, improving memory, decreasing thedegradation of memory, or extending survival; treat demyelinatingdiseases by reducing a symptom of demyelinating diseases or reducing theloss of myelin or increasing the amount of myelin or increasing thelevel of myelin; treat diabetes by decreasing a symptom of diabetes ordecreasing loss of insulin producing cells or decreasing loss ofpancreatic cells or reducing insulin insensitivity; treat cancer bydecreasing a symptom of cancer, or treat neurodegeneration by treating asymptom of neurodegeneration. Symptoms of cancer (e.g. multiple myeloma,cancers of secretory cells), neurodegenerative diseases, demyelinatingdiseases, eye diseases, fibrotic diseases, or diabetes would be known ormay be determined by a person of ordinary skill in the art. The term“treating” and conjugations thereof, include prevention of an injury,pathology, condition, or disease (e.g. preventing the development of oneor more symptoms of cancer, neurodegenerative diseases, demyelinatingdiseases, and/or diabetes).

An “effective amount” is an amount sufficient to accomplish a statedpurpose (e.g. achieve the effect for which it is administered, treat adisease, reduce enzyme activity, increase enzyme activity, reduce one ormore symptoms of a disease or condition). An example of an “effectiveamount” is an amount sufficient to contribute to the treatment,prevention, or reduction of a symptom or symptoms of a disease, whichcould also be referred to as a “therapeutically effective amount.” A“reduction” of a symptom or symptoms (and grammatical equivalents ofthis phrase) means decreasing of the severity or frequency of thesymptom(s), or elimination of the symptom(s). A “prophylacticallyeffective amount” of a drug is an amount of a drug that, whenadministered to a subject, will have the intended prophylactic effect,e.g., preventing or delaying the onset (or reoccurrence) of an injury,disease, pathology or condition, or reducing the likelihood of the onset(or reoccurrence) of an injury, disease, pathology, or condition, ortheir symptoms. The full prophylactic effect does not necessarily occurby administration of one dose, and may occur only after administrationof a series of doses. Thus, a prophylactically effective amount may beadministered in one or more administrations. An “activity decreasingamount,” as used herein, refers to an amount of antagonist (inhibitor)required to decrease the activity of an enzyme or protein relative tothe absence of the antagonist. An “activity increasing amount,” as usedherein, refers to an amount of agonist (activator) required to increasethe activity of an enzyme or protein relative to the absence of theagonist. A “function disrupting amount,” as used herein, refers to theamount of antagonist (inhibitor) required to disrupt the function of anenzyme or protein relative to the absence of the antagonist. A “functionincreasing amount,” as used herein, refers to the amount of agonist(activator) required to increase the function of an enzyme or proteinrelative to the absence of the agonist. The exact amounts will depend onthe purpose of the treatment, and will be ascertainable by one skilledin the art using known techniques (see, e.g., Lieberman, PharmaceuticalDosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technologyof Pharmaceutical Compounding (1999); Pickar, Dosage Calculations(1999); and Remington: The Science and Practice of Pharmacy, 20thEdition, 2003, Gennaro, Ed., Lippincott, Williams & Wilkins).

The term “associated” or “associated with” in the context of a substanceor substance activity or function associated with a disease (e.g. cancer(e.g. multiple myeloma, cancers of secretory cells), neurodegenerativediseases, demyelinating diseases, eye diseases, fibrotic diseases, ordiabetes) means that the disease (e.g. cancer (e.g. multiple myeloma,cancers of secretory cells), neurodegenerative diseases, demyelinatingdiseases, eye diseases, fibrotic diseases, or diabetes) is caused by (inwhole or in part), or a symptom of the disease is caused by (in whole orin part) the substance or substance activity or function. For example, asymptom of a disease or condition associated with an increase in Ire1(e.g. Ire1α) activity may be a symptom that results (entirely orpartially) from an increase in Ire1 (e.g. Ire1α) activity (e.g increasein Ire1 (e.g. Ire1α) phosphorylation or activity of phosphorylated Ire1(e.g. Ire1α) or activity of Ire1 (e.g. Ire1α) or increase in activity ofan Ire1 (e.g. Ire1α) signal transduction or signalling pathway, Ire1(e.g. Ire1α) RNase activity). As used herein, what is described as beingassociated with a disease, if a causative agent, could be a target fortreatment of the disease. For example, a disease associated withincreased Ire1 (e.g. Ire1α) activity or Ire1 (e.g. Ire1α) pathwayactivity (e.g. phosphorylated Ire1 (e.g. Ire1α) activity or pathway),may be treated with an agent (e.g. compound as described herein)effective for decreasing the level of activity of Ire1 (e.g. Ire1α)activity or Ire1 (e.g. Ire1α) pathway or phosphorylated Ire1 (e.g.Ire1α) activity or pathway. For example, a disease associated withphosphorylated Ire1 (e.g. Ire1α), may be treated with an agent (e.g.compound as described herein) effective for decreasing the level ofactivity of phosphorylated Ire1 (e.g. Ire1α) or a downstream componentor effector of phosphorylated Ire1 (e.g. Ire1α). For example, a diseaseassociated with Ire1 (e.g. Ire1α), may be treated with an agent (e.g.compound as described herein) effective for decreasing the level ofactivity of Ire1 (e.g. Ire1α) or a downstream component or effector ofIre1 (e.g. Ire1α).

“Control” or “control experiment” is used in accordance with its plainordinary meaning and refers to an experiment in which the subjects orreagents of the experiment are treated as in a parallel experimentexcept for omission of a procedure, reagent, or variable of theexperiment. In some instances, the control is used as a standard ofcomparison in evaluating experimental effects.

“Contacting” is used in accordance with its plain ordinary meaning andrefers to the process of allowing at least two distinct species (e.g.chemical compounds including biomolecules, or cells) to becomesufficiently proximal to react, interact or physically touch. It shouldbe appreciated, however, that the resulting reaction product can beproduced directly from a reaction between the added reagents or from anintermediate from one or more of the added reagents which can beproduced in the reaction mixture. The term “contacting” may includeallowing two species to react, interact, or physically touch, whereinthe two species may be a compound as described herein and a protein orenzyme (e.g. Ire1 (e.g. Ire1α) or phosphorylated Ire1 (e.g. Ire1α) orcomponent of Ire1 (e.g. Ire1α) pathway or component of phosphorylatedIre1 (e.g. Ire1α) pathway). In some embodiments contacting includesallowing a compound described herein to interact with a protein orenzyme that is involved in a signaling pathway (e.g. Ire1 (e.g. Ire1α)protein or Ire1 (e.g. Ire1α) pathway).

As defined herein, the term “inhibition”, “inhibit”, “inhibiting” andthe like in reference to a protein-inhibitor (e.g. antagonist)interaction means negatively affecting (e.g. decreasing) the activity orfunction of the protein relative to the activity or function of theprotein in the absence of the inhibitor. In some embodiments inhibitionrefers to reduction of a disease or symptoms of disease. In someembodiments, inhibition refers to a reduction in the activity of asignal transduction pathway or signaling pathway. Thus, inhibitionincludes, at least in part, partially or totally blocking stimulation,decreasing, preventing, or delaying activation, or inactivating,desensitizing, or down-regulating signal transduction or enzymaticactivity or the amount of a protein. In some embodiments, inhibitionrefers to a decrease in the activity of a signal transduction pathway orsignaling pathway (e.g. Ire1 (e.g. Ire1α) or phosphorylated Ire1 (e.g.Ire1α) or Ire1 (e.g. Ire1α) pathway or phosphorylated Ire1 (e.g. Ire1α)pathway or pathway activated by Ire1 (e.g. Ire1α) phosphorylation).Thus, inhibition may include, at least in part, partially or totallydecreasing stimulation, decreasing or reducing activation, orinactivating, desensitizing, or down-regulating signal transduction orenzymatic activity or the amount of a protein increased in a disease(e.g. level of Ire1 (e.g. Ire1α) activity or protein or level oractivity of a component of an Ire1 (e.g. Ire1α) pathway or level ofphosphorylated Ire1 (e.g. Ire1α) activity or protein or level oractivity of a component of a phosphorylated Ire1 (e.g. Ire1α) pathway,wherein each is associated with cancer (e.g. multiple myeloma, orcancers of secretory cells), neurodegenerative diseases, demyelinatingdiseases, eye diseases, fibrotic diseases, or diabetes). Inhibition mayinclude, at least in part, partially or totally decreasing stimulation,decreasing or reducing activation, or deactivating, desensitizing, ordown-regulating signal transduction or enzymatic activity or the amountof a protein (e.g. Ire1 (e.g. Ire1α), phosphorylated Ire1 (e.g. Ire1α),protein downstream in a pathway from Ire1 (e.g. Ire1α), proteindownstream in a pathway activated by phosphorylated Ire1 (e.g. Ire1α))that may modulate the level of another protein or increase cell survival(e.g. decrease in phosphorylated Ire1 (e.g. Ire1α) pathway activity mayincrease cell survival in cells that may or may not have an increase inphosphorylated Ire1 (e.g. Ire1α) pathway activity relative to anon-disease control or decrease in Ire1 (e.g. Ire1α) pathway activitymay increase cell survival in cells that may or may not have a increasein Ire1 (e.g. Ire1α) pathway activity relative to a non-diseasecontrol).

As defined herein, the term “activation”, “activate”, “activating” andthe like in reference to a protein-activator (e.g. agonist) interactionmeans positively affecting (e.g. increasing) the activity or function ofthe protein (e.g. Ire1 (e.g. Ire1α), phosphorylated Ire1 (e.g. Ire1α),component of pathway including Ire1 (e.g. Ire1α), or component ofpathway including phosphorylated Ire1 (e.g. Ire1α)) relative to theactivity or function of the protein in the absence of the activator(e.g. compound described herein). In some embodiments, activation refersto an increase in the activity of a signal transduction pathway orsignaling pathway (e.g. Ire1 (e.g. Ire1α) or phosphorylated Ire1 (e.g.Ire1α) pathway). Thus, activation may include, at least in part,partially or totally increasing stimulation, increasing or enablingactivation, or activating, sensitizing, or up-regulating signaltransduction or enzymatic activity or the amount of a protein decreasedin a disease (e.g. level of Ire1 (e.g. Ire1α) activity or level ofprotein or activity decreased by phosphorylation of Ire1 (e.g. Ire1α) orprotein associated with cancer (e.g. multiple myeloma, or cancers ofsecretory cells), neurodegenerative diseases, demyelinating diseases,eye diseases, fibrotic diseases, or diabetes). Activation may include,at least in part, partially or totally increasing stimulation,increasing or enabling activation, or activating, sensitizing, orup-regulating signal transduction or enzymatic activity or the amount ofa protein (e.g. Ire1 (e.g. Ire1α), protein downstream of Ire1 (e.g.Ire1α), protein activated or upregulated by Ire1 (e.g. Ire1α), proteinactivated or upregulated by phosphorylation of Ire1 (e.g. Ire1α)) thatmay modulate the level of another protein or increase cell survival(e.g. increase in Ire1 (e.g. Ire1α) activity may increase cell survivalin cells that may or may not have a reduction in Ire1 (e.g. Ire1α)activity relative to a non-disease control).

The term “modulator” refers to a composition that increases or decreasesthe level of a target molecule or the function of a target molecule. Insome embodiments, a modulator of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α)pathway or phosphorylation of Ire1 (e.g. Ire1α) or pathway activated byphosphorylation of Ire1 (e.g. Ire1α) is a compound that reduces theseverity of one or more symptoms of a disease associated with Ire1 (e.g.Ire1α) or Ire1 (e.g. Ire1α) pathway (e.g. disease associated with anincrease in the level of Ire1 (e.g. Ire1α) activity or protein or Ire1(e.g. Ire1α) pathway activity or protein or Ire1 (e.g. Ire1α)phosphorylation or pathway activated by Ire1 (e.g. Ire1α)phosphorylation, for example cancer (e.g. multiple myeloma, or cancersof secretory cells), neurodegenerative diseases, demyelinating diseases,eye diseases, fibrotic diseases, or diabetes) or a disease that is notcaused by Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α) pathway but may benefitfrom modulation of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α) pathwayactivity (e.g. decreasing in level or level of activity of Ire1 (e.g.Ire1α) or Ire1 (e.g. Ire1α) pathway). In embodiments, a modulator ofIre1 (e.g. Ire1α) or Ire1 (e.g. Ire1α) pathway (e.g. phosphorylated Ire1(e.g. Ire1α) or phosphorylated Ire1 (e.g. Ire1α) pathway) is ananti-cancer agent. In embodiments, a modulator of Ire1 (e.g. Ire1α) orIre1 (e.g. Ire1α) pathway (e.g. phosphorylated Ire1 (e.g. Ire1α) orphosphorylated Ire1 (e.g. Ire1α) pathway) is a neuroprotectant. Inembodiments, a modulator of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α)pathway (e.g. phosphorylated Ire1 (e.g. Ire1α) or phosphorylated Ire1(e.g. Ire1α) pathway) is an anti-demyelinating agent. In embodiments, amodulator of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α) pathway is a memoryenhancing agent. In embodiments, a modulator of Ire1 (e.g. Ire1α) orIre1 (e.g. Ire1α) pathway (e.g. phosphorylated Ire1 (e.g. Ire1α) orphosphorylated Ire1 (e.g. Ire1α) pathway) is an anti-diabetic agent. Inembodiments, a modulator of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α)pathway (e.g. phosphorylated Ire1 (e.g. Ire1α) or phosphorylated Ire1(e.g. Ire1α) pathway) is an anti-eye disease agent. In embodiments, amodulator of Ire1 (e.g. Ire1α) or Ire1 (e.g. Ire1α) pathway (e.g.phosphorylated Ire1 (e.g. Ire1α) or phosphorylated Ire1 (e.g. Ire1α)pathway) is an anti-fibrosis agent.

“Patient” or “subject in need thereof” refers to a living organismsuffering from or prone to a disease or condition that can be treated byadministration of a compound or pharmaceutical composition, as providedherein. Non-limiting examples include humans, other mammals, bovines,rats, mice, dogs, monkeys, goat, sheep, cows, deer, and othernon-mammalian animals. In some embodiments, a patient is human. In someembodiments, a patient is an ape. In some embodiments, a patient is amonkey. In some embodiments, a patient is a mouse. In some embodiments,a patient is an experimental animal. In some embodiments, a patient is arat. In some embodiments, a patient is a test animal. In someembodiments, a patient is a newborn animal. In some embodiments, apatient is a newborn human. In some embodiments, a patient is a juvenileanimal. In some embodiments, a patient is a juvenile human. In someembodiments, a patient is a newborn mammal. In some embodiments, apatient is an elderly animal. In some embodiments, a patient is anelderly human. In some embodiments, a patient is an elderly mammal. Insome embodiments, a patient is a geriatric patient.

“Disease” or “condition” refer to a state of being or health status of apatient or subject capable of being treated with a compound,pharmaceutical composition, or method provided herein. In someembodiments, the disease is a disease related to (e.g. caused by) anincrease in the level of Ire1 (e.g. Ire1α), Ire1 (e.g. Ire1α)phosphorylation, Ire1 (e.g. Ire1α) RNase activity, or Ire1 (e.g. Ire1α)pathway activity, or pathway activated by phosphorylation of Ire1 (e.g.Ire1α). In some embodiments, the disease is a disease related to (e.g.caused by) neurodegeneration. In some embodiments, the disease is adisease related to (e.g. caused by) neural cell death. In someembodiments, the disease is a disease related to (e.g. caused by) celldeath. In some embodiments, the disease is a disease related to (e.g.caused by) pancreatic cell death. In some embodiments, the disease is adisease related to (e.g. caused by) insulin-producing cell death. Insome embodiments, the disease is a disease related to (e.g. caused by)loss of myelin. In some embodiments, the disease is a disease related to(e.g. caused by) reduction in myelin. In some embodiments, the diseaseis a disease related to (e.g. caused by) an increase in the level ofIre1 (e.g. Ire1α) activity (e.g. RNase activity), Ire1 (e.g. Ire1α)phosphorylation, Ire1 (e.g. Ire1α) pathway activity, or phosphorylatedIre1 (e.g. Ire1α) pathway activity. In some embodiments, the disease iscancer (e.g. multiple myeloma or cancers of secretory cells). In someembodiments, the disease is a neurodegenerative disease. In someembodiments, the disease is a demyelinating disease. In someembodiments, the disease is diabetes. In some embodiments, the diseaseis an interstitial lung disease (ILD). In some embodiments, the diseaseis idiopathic pulmonary fibrosis (IPF). In some embodiments, the diseaseis a fibrotic disease. In some embodiments, the disease is an eyedisease (e.g., disease causing vision impairment).

Examples of diseases, disorders, or conditions include, but are notlimited to, cancer (e.g. multiple myeloma or cancers of secretorycells), neurodegenerative diseases, demyelinating diseases, eyediseases, fibrotic diseases, and diabetes. In some instances, “disease”or “condition” refers to cancer. In some further instances, “cancer”refers to human cancers and carcinomas, sarcomas, adenocarcinomas,lymphomas, leukemias, melanomas, etc., including solid and lymphoidcancers, kidney, breast, lung, bladder, colon, ovarian, prostate,pancreas, stomach, brain, head and neck, skin, uterine, testicular,glioma, esophagus, liver cancer, including hepatocarcinoma, lymphoma,including B-acute lymphoblastic lymphoma, non-Hodgkin's lymphomas (e.g.,Burkitt's, Small Cell, and Large Cell lymphomas), Hodgkin's lymphoma,leukemia (including AML, ALL, and CML), and/or multiple myeloma.

As used herein, the term “cancer” refers to all types of cancer,neoplasm or malignant tumors found in mammals, including leukemia,lymphoma, carcinomas and sarcomas. Exemplary cancers that may be treatedwith a compound, pharmaceutical composition, or method provided hereininclude multiple myeloma, blood cancers, lymphoma, sarcoma, bladdercancer, bone cancer, brain tumor, cervical cancer, colon cancer,esophageal cancer, gastric cancer, head and neck cancer, kidney cancer,myeloma, thyroid cancer, leukemia, prostate cancer, breast cancer (e.g.ER positive, ER negative, chemotherapy resistant, herceptin resistant,HER2 positive, doxorubicin resistant, tamoxifen resistant, ductalcarcinoma, lobular carcinoma, primary, metastatic), ovarian cancer,pancreatic cancer, liver cancer (e.g.hepatocellular carcinoma), lungcancer (e.g. non-small cell lung carcinoma, squamous cell lungcarcinoma, adenocarcinoma, large cell lung carcinoma, small cell lungcarcinoma, carcinoid, sarcoma), glioblastoma multiforme, glioma, ormelanoma. Additional examples include, cancer of the thyroid, endocrinesystem, brain, breast, cervix, colon, head & neck, liver, kidney, lung,non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach,uterus or Medulloblastoma, Hodgkin's Disease, Non-Hodgkin's Lymphoma,multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme,ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primarymacroglobulinemia, primary brain tumors, cancer, malignant pancreaticinsulanoma, malignant carcinoid, urinary bladder cancer, premalignantskin lesions, testicular cancer, lymphomas, thyroid cancer,neuroblastoma, esophageal cancer, genitourinary tract cancer, malignanthypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms ofthe endocrine or exocrine pancreas, medullary thyroid cancer, medullarythyroid carcinoma, melanoma, colorectal cancer, papillary thyroidcancer, hepatocellular carcinoma, Paget's Disease of the Nipple,Phyllodes Tumors, Lobular Carcinoma, Ductal Carcinoma, cancer of thepancreatic stellate cells, cancer of the hepatic stellate cells, orprostate cancer.

The term “leukemia” refers broadly to progressive, malignant diseases ofthe blood-forming organs and is generally characterized by a distortedproliferation and development of leukocytes and their precursors in theblood and bone marrow. Leukemia is generally clinically classified onthe basis of (1) the duration and character of the disease-acute orchronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid(lymphogenous), or monocytic; and (3) the increase or non-increase inthe number abnormal cells in the blood-leukemic or aleukemic(subleukemic). Exemplary leukemias that may be treated with a compound,pharmaceutical composition, or method provided herein include, forexample, acute nonlymphocytic leukemia, chronic lymphocytic leukemia,acute granulocytic leukemia, chronic granulocytic leukemia, acutepromyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, aleukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovineleukemia, chronic myelocytic leukemia, leukemia cutis, embryonalleukemia, eosinophilic leukemia, Gross' leukemia, hairy-cell leukemia,hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia,stem cell leukemia, acute monocytic leukemia, leukopenic leukemia,lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia,lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia,mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia,monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloidgranulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasmacell leukemia, multiple myeloma, plasmacytic leukemia, promyelocyticleukemia, Rieder cell leukemia, Schilling's leukemia, stem cellleukemia, subleukemic leukemia, or undifferentiated cell leukemia.

The term “sarcoma” generally refers to a tumor which is made up of asubstance like the embryonic connective tissue and is generally composedof closely packed cells embedded in a fibrillar or homogeneoussubstance. Sarcomas that may be treated with a compound, pharmaceuticalcomposition, or method provided herein include a chondrosarcoma,fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma,Abemethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft partsarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma,chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrialsarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblasticsarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma,idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcomaof B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen'ssarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma,leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma,reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovialsarcoma, or telangiectaltic sarcoma.

The term “melanoma” is taken to mean a tumor arising from themelanocytic system of the skin and other organs. Melanomas that may betreated with a compound, pharmaceutical composition, or method providedherein include, for example, acral-lentiginous melanoma, amelanoticmelanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma,Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma,malignant melanoma, nodular melanoma, subungal melanoma, or superficialspreading melanoma.

The term “carcinoma” refers to a malignant new growth made up ofepithelial cells tending to infiltrate the surrounding tissues and giverise to metastases. Exemplary carcinomas that may be treated with acompound, pharmaceutical composition, or method provided herein include,for example, medullary thyroid carcinoma, familial medullary thyroidcarcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma,adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenalcortex, alveolar carcinoma, alveolar cell carcinoma, basal cellcarcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamouscell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma,bronchogenic carcinoma, cerebriform carcinoma, cholangiocellularcarcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma,corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinomacutaneum, cylindrical carcinoma, cylindrical cell carcinoma, ductcarcinoma, ductal carcinoma, carcinoma durum, embryonal carcinoma,encephaloid carcinoma, epiermoid carcinoma, carcinoma epithelialeadenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum,gelatiniforni carcinoma, gelatinous carcinoma, giant cell carcinoma,carcinoma gigantocellulare, glandular carcinoma, granulosa cellcarcinoma, hair-matrix carcinoma, hematoid carcinoma, hepatocellularcarcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroidcarcinoma, infantile embryonal carcinoma, carcinoma in situ,intraepidermal carcinoma, intraepithelial carcinoma, Krompecher'scarcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma, lenticularcarcinoma, carcinoma lenticulare, lipomatous carcinoma, lobularcarcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullarycarcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma,carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma,carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes,nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans,osteoid carcinoma, papillary carcinoma, periportal carcinoma,preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma,renal cell carcinoma of kidney, reserve cell carcinoma, carcinomasarcomatodes, schneiderian carcinoma, scirrhous carcinoma, carcinomascroti, signet-ring cell carcinoma, carcinoma simplex, small-cellcarcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cellcarcinoma, carcinoma spongiosum, squamous carcinoma, squamous cellcarcinoma, string carcinoma, carcinoma telangiectaticum, carcinomatelangiectodes, transitional cell carcinoma, carcinoma tuberosum,tubular carcinoma, tuberous carcinoma, verrucous carcinoma, or carcinomavillosum.

As used herein, the term “neurodegenerative disease” refers to a diseaseor condition in which the function of a subject's nervous system becomesimpaired (e.g. relative to a control subject who does not have theneurodegenerative disease). Examples of neurodegenerative diseases thatmay be treated with a compound, pharmaceutical composition, or methoddescribed herein include Alexander's disease, Alper's disease,Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxiatelangiectasia, Batten disease (also known asSpielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiformencephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasaldegeneration, Creutzfeldt-Jakob disease, frontotemporal dementia,Gerstmann-Straussler-Scheinker syndrome, Huntington's disease,HIV-associated dementia, Kennedy's disease, Krabbe's disease, kuru, Lewybody dementia, Machado-Joseph disease (Spinocerebellar ataxia type 3),Multiple sclerosis, Multiple System Atrophy, Narcolepsy,Neuroborreliosis, Parkinson's disease, Pelizaeus-Merzbacher Disease,Pick's disease, Primary lateral sclerosis, Prion diseases, Refsum'sdisease, Sandhoffs disease, Schilder's disease, Subacute combineddegeneration of spinal cord secondary to Pernicious Anaemia,Schizophrenia, Spinocerebellar ataxia (multiple types with varyingcharacteristics), Spinal muscular atrophy, Steele-Richardson-Olszewskidisease, Wolfram Syndrome, transverse myelitis, Charcot-Marie-Tooth(CMT) disease, or Tabes dorsalis. Examples of neurodegenerative diseasesthat may be treated with a compound, pharmaceutical composition, ormethod described herein include retinitis pigmentosa, amyotrophiclateral sclerosis, retinal degeneration, macular degeneration,Parkinson's Disease, Alzheimer Disease, Huntington's Disease, PrionDisease, Creutzfeldt-Jakob Disease, or Kuru.

As used herein, the term “demyelinating disease” refers to a disease orcondition is which the myelin sheath of a subject's neurons is orbecomes impaired (e.g. relative to a control subject who does not havethe demyelinating disease). Examples of demyelinating disease that maybe treated with a compound, pharmaceutical composition, or methoddescribed herein include Wolfram Syndrome, Pelizaeus-Merzbacher Disease,Transverse Myelitis, Charcot-Marie-Tooth Disease, and MultipleSclerosis.

As used herein, the term “diabetes” or “diabetes mellitus” refers to adisease or condition is which a subject has high blood sugar. Examplesof diabetes that may be treated with a compound, pharmaceuticalcomposition, or method described herein include type I diabetes (type Idiabetes mellitus), which is characterized by the subject's failure toproduce insulin or failure to produce sufficient insulin for thesubject's metabolic needs; type II diabetes (type II diabetes mellitus),which is characterized by insulin resistance (i.e. the failure of thesubject (e.g. subject's cells) to use insulin properly; and gestationaldiabetes, which is high blood sugar during pregnancy. In embodiments,diabetes is type I diabetes. In embodiments, diabetes is type IIdiabetes. In embodiments, diabetes is gestational diabetes. Inembodiments, diabetes is a disease or condition in which a subject hashigh blood sugar as determined by an AlC test (e.g. 6.5% or greater),fasting plasma glucose test (e.g. 126 mg/dL or greater), or oral glucosetolerance test (e.g. 200 mg/dL or greater). In embodiments, the diabetesis associated with Wolfram Syndrome.

As used herein, the term “eye disease” or “disease causing visionimpairment” refers to a disease or condition is which the function of asubject's eye or eyes is impaired (e.g. relative to a subject withoutthe disease). Examples of eye diseases that may be treated with acompound, pharmaceutical composition, or method described herein includeretinitis pigmentosa, retinal degeneration, macular degeneration, andWolfram Syndrome.

As used herein, the term “fibrosis” refers to the formation of excessfibrous connective tissue. The term “fibrotic disease” refers to adisease or condition caused by aberrant fibrosis or a disease orcondition in which a symptom is aberrant fibrosis (e.g. relative to acontrol subject without the disease). Examples of fibrotic diseases thatmay be treated with a compound, pharmaceutical composition, or methoddescribed herein include idiopathic pulmonary fibrosis (IPF), myocardialinfarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen(Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis(fatty liver disease), and hepatic fibrosis.

The term “signaling pathway” as used herein refers to a series ofinteractions between cellular and optionally extra-cellular components(e.g. proteins, nucleic acids, small molecules, ions, lipids) thatconveys a change in one component to one or more other components, whichin turn may convey a change to additional components, which isoptionally propagated to other signaling pathway components.

“Pharmaceutically acceptable excipient” and “pharmaceutically acceptablecarrier” refer to a substance that aids the administration of an activeagent to and absorption by a subject and can be included in thecompositions of the present invention without causing a significantadverse toxicological effect on the patient. Non-limiting examples ofpharmaceutically acceptable excipients include water, NaCl, normalsaline solutions, lactated Ringer's, normal sucrose, normal glucose,binders, fillers, disintegrants, lubricants, coatings, sweeteners,flavors, salt solutions (such as Ringer's solution), alcohols, oils,gelatins, carbohydrates such as lactose, amylose or starch, fatty acidesters, hydroxymethycellulose, polyvinyl pyrrolidine, mannitol, gumacacia, calcium phosphate, alginates, tragacanth, calcium silicate,microcrystalline cellulose, cellulose, syrup, and methyl cellulose,colors, and the like. The formulations can additionally include:lubricating agents such as talc, magnesium stearate, and mineral oil;wetting agents; emulsifying and suspending agents; preserving agentssuch as methyl and propylhydroxy benzoates; sweetening agents; andflavoring agents. The compositions described herein can be formulated soas to provide quick, sustained or delayed release of the activeingredient after administration to the patient by employing proceduresknown in the art. Such preparations can be sterilized and, if desired,mixed with auxiliary agents such as lubricants, preservatives,stabilizers, wetting agents, emulsifiers, salts for influencing osmoticpressure, buffers, coloring, and/or aromatic substances and the likethat do not deleteriously react with the compounds of the invention. Oneof skill in the art will recognize that other pharmaceutical excipientsare useful in the present invention.

The term “preparation” is intended to include the formulation of theactive compound with encapsulating material as a carrier providing acapsule in which the active component with or without other carriers, issurrounded by a carrier, which is thus in association with it.Similarly, cachets and lozenges are included. Tablets, powders,capsules, pills, cachets, and lozenges can be used as solid dosage formssuitable for oral administration.

As used herein, the term “administering” means administration by anyroute, including systemic, local, oral administration, administration asa suppository, topical contact, intravenous, parenteral,intraperitoneal, intramuscular, intralesional, intrathecal,intracranial, intranasal or subcutaneous administration, topical(including ophthalmic and to mucous membranes including intranasal,vaginal and rectal delivery), pulmonary (e.g., by inhalation orinsufflation of powders or aerosols, including by nebulizer;intratracheal, intranasal, epidermal and transdermal), transmucosal(e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, ortransdermal), ocular, or the implantation of a slow-release device,e.g., a mini-osmotic pump, to a subject. Parenteral administrationincludes, e.g., intravenous, intraarterial, intramuscular,intra-arteriole, intradermal, subcutaneous, intraperitoneal,intrathecal, intraventricular, and intracranial. Parenteraladministration can be in the form of a single bolus dose, or may be, forexample, by a continuous perfusion pump. Pharmaceutical compositions andformulations for topical administration may include transdermal patches,ointments, lotions, creams, gels, drops, suppositories, sprays, liquidsand powders. Methods for ocular delivery can include topicaladministration (eye drops), subconjunctival, periocular or intravitrealinjection or introduction by balloon catheter or ophthalmic insertssurgically placed in the conjunctival sac. Other modes of deliveryinclude, but are not limited to, the use of liposomal formulations,intravenous infusion, transdermal patches, etc. By “co-administer” it ismeant that a composition described herein is administered at the sametime, just prior to, or just after the administration of one or moreadditional therapies (e.g. anti-cancer agent, chemotherapeutic,treatment for an eye disease, treatment for fibrosis, treatment for ademyelinating disease, diabetes treatment, or treatment for aneurodegenerative disease). The compound of the invention can beadministered alone or can be coadministered to the patient. Thecompositions (e.g. compounds) described herein can also be formulated incombination with one or more additional active ingredients which caninclude any pharmaceutical agent such as anti viral agents, vaccines,antibodies, immune enhancers, immune suppressants, anti inflammatoryagents and the like. Coadministration is meant to include simultaneousor sequential administration of the compound individually or incombination (more than one compound or agent). Thus, the preparationscan also be combined, when desired, with other active substances (e.g.to reduce metabolic degradation). The compositions of the presentinvention can be delivered by transdermally, by a topical route,formulated as applicator sticks, solutions, suspensions, emulsions,gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.Oral preparations include tablets, pills, powder, dragees, capsules,liquids, lozenges, cachets, gels, syrups, slurries, suspensions, etc.,suitable for ingestion by the patient. Solid form preparations includepowders, tablets, pills, capsules, cachets, suppositories, anddispersible granules. Liquid form preparations include solutions,suspensions, and emulsions, for example, water or water/propylene glycolsolutions. The compositions of the present invention may additionallyinclude components to provide sustained release and/or comfort. Suchcomponents include high molecular weight, anionic mucomimetic polymers,gelling polysaccharides and finely-divided drug carrier substrates.These components are discussed in greater detail in U.S. Pat. Nos.4,911,920; 5,403,841; 5,212,162; and 4,861,760. The entire contents ofthese patents are incorporated herein by reference in their entirety forall purposes. The compositions of the present invention can also bedelivered as microspheres for slow release in the body. For example,microspheres can be administered via intradermal injection ofdrug-containing microspheres, which slowly release subcutaneously (seeRao, J. Biomater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable andinjectable gel formulations (see, e.g., Gao Pharm. Res. 12:857-863,1995); or, as microspheres for oral administration (see, e.g., Eyles, J.Pharm. Pharmacol. 49:669-674, 1997). In another embodiment, theformulations of the compositions of the present invention can bedelivered by the use of liposomes which fuse with the cellular membraneor are endocytosed, i.e., by employing receptor ligands attached to theliposome, that bind to surface membrane protein receptors of the cellresulting in endocytosis. By using liposomes, particularly where theliposome surface carries receptor ligands specific for target cells, orare otherwise preferentially directed to a specific organ, one can focusthe delivery of the compositions of the present invention into thetarget cells in vivo. (See, e.g., Al-Muhammed, J. Microencapsul.13:293-306, 1996; Chonn, Curr. Opin. Biotechnol. 6:698-708, 1995; Ostro,Am. J. Hosp. Pharm. 46:1576-1587, 1989). The compositions of the presentinvention can also be delivered as nanoparticles.

Pharmaceutical compositions provided by the present invention includecompositions wherein the active ingredient (e.g. compounds describedherein, including embodiments or examples) is contained in atherapeutically effective amount, i.e., in an amount effective toachieve its intended purpose. The actual amount effective for aparticular application will depend, inter alia, on the condition beingtreated. When administered in methods to treat a disease, suchcompositions will contain an amount of active ingredient effective toachieve the desired result, e.g., modulating the activity of a targetmolecule (e.g. Ire1 (e.g. Ire1 α) or component of Ire1 (e.g. Ire1 α)signal transduction pathway or component of phosphorylated Ire1 (e.g.Ire1 α) pathway), and/or reducing, eliminating, or slowing theprogression of disease symptoms (e.g. symptoms of cancer (e.g. multiplemyeloma or cancers of secretory cells), neurodegenerative diseases,demyelinating diseases, eye diseases, fibrotic diseases, or diabetes).Determination of a therapeutically effective amount of a compound of theinvention is well within the capabilities of those skilled in the art,especially in light of the detailed disclosure herein.

The dosage and frequency (single or multiple doses) administered to amammal can vary depending upon a variety of factors, for example,whether the mammal suffers from another disease, and its route ofadministration; size, age, sex, health, body weight, body mass index,and diet of the recipient; nature and extent of symptoms of the diseasebeing treated (e.g. symptoms of cancer (e.g. multiple myeloma or cancersof secretory cells), neurodegenerative diseases, demyelinating diseases,eye diseases, fibrotic diseases, or diabetes), kind of concurrenttreatment, complications from the disease being treated or otherhealth-related problems. Other therapeutic regimens or agents can beused in conjunction with the methods and compounds of Applicants'invention. Adjustment and manipulation of established dosages (e.g.,frequency and duration) are well within the ability of those skilled inthe art.

For any compound described herein, the therapeutically effective amountcan be initially determined from cell culture assays. Targetconcentrations will be those concentrations of active compound(s) thatare capable of achieving the methods described herein, as measured usingthe methods described herein or known in the art.

As is well known in the art, therapeutically effective amounts for usein humans can also be determined from animal models. For example, a dosefor humans can be formulated to achieve a concentration that has beenfound to be effective in animals. The dosage in humans can be adjustedby monitoring compounds effectiveness and adjusting the dosage upwardsor downwards, as described above. Adjusting the dose to achieve maximalefficacy in humans based on the methods described above and othermethods is well within the capabilities of the ordinarily skilledartisan.

Dosages may be varied depending upon the requirements of the patient andthe compound being employed. The dose administered to a patient, in thecontext of the present invention should be sufficient to effect abeneficial therapeutic response in the patient over time. The size ofthe dose also will be determined by the existence, nature, and extent ofany adverse side-effects. Determination of the proper dosage for aparticular situation is within the skill of the practitioner. Generally,treatment is initiated with smaller dosages which are less than theoptimum dose of the compound. Thereafter, the dosage is increased bysmall increments until the optimum effect under circumstances isreached.

Dosage amounts and intervals can be adjusted individually to providelevels of the administered compound effective for the particularclinical indication being treated. This will provide a therapeuticregimen that is commensurate with the severity of the individual'sdisease state.

Utilizing the teachings provided herein, an effective prophylactic ortherapeutic treatment regimen can be planned that does not causesubstantial toxicity and yet is effective to treat the clinical symptomsdemonstrated by the particular patient. This planning should involve thecareful choice of active compound by considering factors such ascompound potency, relative bioavailability, patient body weight,presence and severity of adverse side effects, preferred mode ofadministration and the toxicity profile of the selected agent.

The compounds described herein can be used in combination with oneanother, with other active agents known to be useful in treating cancer(e.g. multiple myeloma or cancers of secretory cells), neurodegenerativediseases, demyelinating diseases, eye diseases, fibrotic diseases, ordiabetes, or with adjunctive agents that may not be effective alone, butmay contribute to the efficacy of the active agent.

In some embodiments, co-administration includes administering one activeagent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a secondactive agent. Co-administration includes administering two active agentssimultaneously, approximately simultaneously (e.g., within about 1, 5,10, 15, 20, or 30 minutes of each other), or sequentially in any order.In some embodiments, co-administration can be accomplished byco-formulation, i.e., preparing a single pharmaceutical compositionincluding both active agents. In other embodiments, the active agentscan be formulated separately. In another embodiment, the active and/oradjunctive agents may be linked or conjugated to one another. In someembodiments, the compounds described herein may be combined withtreatments for cancer (e.g. multiple myeloma or cancers of secretorycells), neurodegenerative diseases, demyelinating diseases, or diabetes,such as surgery.

The term “Ire1” or “Ire1α” or “ERN1” refers to the protein“Serine/threonine-protein kinase/endoribonuclease IRE1” a.k.a.“Endoplasmic reticulum to nucleus signaling 1”. In embodiments, “Ire1”or “Ire1α” or “ERN1” refers to the human protein. Included in the term“Ire1” or “Ire1” or “ERN1” are the wildtype and mutant forms of theprotein. In embodiments, “Ire1” or “Ire1α” or “ERN1” refers to theprotein associated with Entrez Gene 2081, OMIM 604033, UniProt 075460,and/or RefSeq (protein) NM_001433. In embodiments, the reference numbersimmediately above refer to the protein, and associated nucleic acids,known as of the date of filing of this application. In embodiments,“Ire1” or “Ire1α” or “ERN1” refers to the wildtype human protein. Inembodiments, “Ire1” or “Ire1α” or “ERN1” refers to the wildtype humannucleic acid.

“Anti-cancer agent” is used in accordance with its plain ordinarymeaning and refers to a composition (e.g. compound, drug, antagonist,inhibitor, modulator) having antineoplastic properties or the ability toinhibit the growth or proliferation of cells. In some embodiments, ananti-cancer agent is a chemotherapeutic. In some embodiments, ananti-cancer agent is an agent identified herein having utility inmethods of treating cancer. In some embodiments, an anti-cancer agent isan agent approved by the FDA or similar regulatory agency of a countryother than the USA, for treating cancer. Examples of anti-cancer agentsinclude, but are not limited to, MEK inhibitors, alkylating agents,anti-metabolites, plant alkaloids, topoisomerase inhibitors, antitumorantibiotics, platinum-based compounds, adrenocortical suppressants,epipodophyllotoxins, antibiotics, enzymes, inhibitors ofmitogen-activated protein kinase signaling, antibodies, doxorubicin,vincristine, etoposide, gemcitabine, imatinib (Gleevec®), agents thatarrest cells in the G2-M phases and/or modulate the formation orstability of microtubules (e.g. Taxol™ (i.e. paclitaxel), steroids,aromatase inhibitors, gonadotropin-releasing hormone agonists (GnRH),adrenocorticosteroids, progestins, estrogens, antiestrogens, androgens,antiandrogens, immunotoxins, radioimmunotherapy, or the like.

“Chemotherapeutic” or “chemotherapeutic agent” is used in accordancewith its plain ordinary meaning and refers to a chemical composition orcompound having antineoplastic properties or the ability to inhibit thegrowth or proliferation of cells.

Additionally, the compounds described herein can be co-administered withconventional immunotherapeutic agents including, but not limited to,immunostimulants (e.g., Bacillus Calmette-Guerin (BCG), levamisole,interleukin-2, alpha-interferon, etc.), monoclonal antibodies (e.g.,anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti-VEGF monoclonalantibodies), immunotoxins (e.g., anti-CD33 monoclonalantibody-calicheamicin conjugate, anti-CD22 monoclonalantibody-pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy(e.g., anti-CD20 monoclonal antibody conjugated to ¹¹¹In, ⁹⁰Y, or ¹³¹I,etc.).

In a further embodiment, the compounds described herein can beco-administered with conventional radiotherapeutic agents including, butnot limited to, radionuclides such as ⁴⁷Sc, ⁶⁴Cu, ⁶⁷Cu, ⁸⁹Sr, ⁸⁶Y, ⁸⁷,Y⁹⁰, Y¹⁰⁵Rh, ¹¹¹Ag, ¹¹¹In, ^(117m)Sn, ¹⁴⁹Pm, ¹⁵³Sm, ¹⁶⁶Ho, ¹⁷⁷Lu, ¹⁸⁶Re,¹⁸⁸Re, ²¹¹At, and ²¹²Bi, optionally conjugated to antibodies directedagainst tumor antigens.

“Anti-diabetic agent” or “antidiabetic agent” is used in accordance withits plain ordinary meaning and refers to a composition (e.g. compound,drug, antagonist, inhibitor, modulator) having the ability to lowerblood glucose levels in a subject. In some embodiments, an anti-diabeticagent is an agent identified herein having utility in methods oftreating diabetes. In some embodiments, an anti-diabetic agent is anagent approved by the FDA or similar regulatory agency of a countryother than the USA, for treating diabetes. Examples of anti-diabeticagents include, but are not limited to, insulin, insulin sensitizers(e.g. biguanides (e.g. metformin, phenformin, or buformin),thiazolidinediones (e.g. rosiglitazone, pioglitazone, troglitazone)),secretagogues (e.g. sulfonylureas (e.g. tolbutamide, acetohexamide,tolazamide, chlorpropamide, glipizide, glyburide, glibenclamide,glimepiride, gliclazide, glycopyramide, gliquidone), meglitinides (e.g.repaglinide, nateglinide)), alpha-glucosidase inhibitors (e.g. miglitol,acarbose, voglibose), peptide analog antidiabetic agents (e.g. incretins(glucagon-like peptide-1, gastric inhibitory peptide), glucagon-likepeptide agonists (e.g. exenatide, liraglutide, taspoglutide), gastricinhibitoty peptide analogs, or dipeptidyl peptidase-4 inhibitors (e.g.vildagliptin, sitagliptin, saxagliptin, linagliptin, allogliptin,septagliptin), amylin agonist analogues (e.g. pramlintide).

B. Compositions

In an aspect is provided a compound, or a pharmaceutically acceptablesalt thereof, having the formula:

wherein, ring A is substituted or unsubstituted cycloalkylene,substituted or unsubstituted heterocycloalkylene, substituted orunsubstituted arylene, or substituted or unsubstituted heteroarylene; L¹is a bond or unsubstituted C₁-C₅ alkylene; L² is a bond, —NR^(6a)—, —O—,—S—, —C(O)—, —S(O)—, —S(O)₂—, —NR^(6a)C(O)—, —C(O)(CH₂)_(z2)—,—C(O)NR^(6b)—, —NR^(6a)C(O)O—, —NR^(6a)C(O)NR^(6b)—, substituted orunsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene; R¹ is hydrogen, oxo,halogen, —CX₃, —CN, —SO₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)m, —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO_(n)R¹⁰, —NR^(7b)C═(O)R⁹, —NR^(7b)C(O)OR⁹,—NR⁷OR⁹, —OCX^(b) ₃, —OCHX₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl; R² ishydrogen, oxo, halogen, —CX^(a) ₃, —CN, —SO₂Cl, —SO_(n1)R^(10a),SO_(v1)NR^(7a)R^(8a), —NNH₂, —ONR^(7a)R^(8a), —NHC═(O)NHNH₂,—NHC═(O)NR^(7a)R^(8a), —N(O)mi, —NR^(7a)R^(8a)—C(O)R^(9a), —C(O)OR^(9a),—C(O)NR^(7a)R^(8a), —OR^(10a)—, NR^(7a)SO_(n1)R^(8a),—NR^(7a)C═(O)R^(9a), —NR^(7a)C(O)OR^(9a), —NR^(7a)OR^(9a), —OCX^(a) ₃,—OCHX^(a) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R³ isindependently hydrogen, oxo, halogen, —CX^(b) ₃, —CN, —SO₂Cl,—SO_(n2)R^(10b), —SO₂NR^(7b)R^(8b), —NHNH₂, —ONR^(7b)R^(8b),—NHC═(O)NHNH₂,—NHC═(O)NR^(7b)R^(8b), —N(O)_(m2), —NR^(7b)R^(8b), —C(O)R^(9b),—C(O)—OR^(9b), —C(O)NR^(7b)R^(8b), —OR^(10b), —NR^(7b)SO_(n2)R^(10b),—NR^(7b)C═(O)R^(9b), —NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —CX^(b) ₃,—OCHX^(b) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁴ andR⁵ are independently hydrogen or unsubstituted C₁-C₆ alkyl; R⁷, R⁸, R⁹,R¹⁰, R^(6a), R^(7a), R^(8a), R^(9a), R^(10a), R^(6b), R^(7b), R^(8b),R^(9b) and R^(10b) are independently hydrogen, halogen, —CF₃, —CN, —OH,—NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁷ andR⁸ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7b) and R^(8b) substituents bonded to thesame nitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; each occurrence of the symbols n, n1, and n2 isindependently an integer from 0 to 4; each occurrence of the symbols m,m1, m2, v, v1, and v2 is independently an integer from 1 to 2; thesymbol z is an integer from 0 to 2; the symbol z2 is an integer from 1to 4; and each occurrence of the symbols X, X^(a), and X^(b) isindependently a halogen.

In embodiments, ring A is substituted or unsubstituted monocycliccycloalkylene, substituted or unsubstituted monocyclicheterocycloalkylene, substituted or unsubstituted monocyclic arylene, orsubstituted or unsubstituted monocyclic heteroarylene. In embodiments,ring A is substituted monocyclic cycloalkylene, substituted monocyclicheterocycloalkylene, substituted monocyclic arylene, or substitutedmonocyclic heteroarylene. In embodiments, ring A is unsubstitutedmonocyclic cycloalkylene, unsubstituted monocyclic heterocycloalkylene,unsubstituted monocyclic arylene, or unsubstituted monocyclicheteroarylene.

In embodiments, ring A is substituted or unsubstituted C₃-C₈cycloalkylene, substituted or unsubstituted 3 to 8 memberedheterocycloalkylene, substituted or unsubstituted C₆-C₁₀ arylene, orsubstituted or unsubstituted 5 to 10 membered heteroarylene. Inembodiments, ring A is substituted C₃-C₈ cycloalkylene, substituted 3 to8 membered heterocycloalkylene, substituted C₆-C₁₀ arylene, orsubstituted 5 to 10 membered heteroarylene. In embodiments, ring A isunsubstituted C₃-C₈ cycloalkylene, unsubstituted 3 to 8 memberedheterocycloalkylene, unsubstituted C₆-C₁₀ arylene, or unsubstituted 5 to10 membered heteroarylene. In embodiments, ring A is substituted orunsubstituted C₃-C₆ cycloalkylene, substituted or unsubstituted 3 to 6membered heterocycloalkylene, substituted or unsubstituted C₆-C₁₀arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.In embodiments, ring A is substituted C₃-C₆ cycloalkylene, substituted 3to 6 membered heterocycloalkylene, substituted C₆-C₁₀ arylene, orsubstituted 5 to 9 membered heteroarylene. In embodiments, ring A isunsubstituted C₃-C₆ cycloalkylene, unsubstituted 3 to 6 memberedheterocycloalkylene, unsubstituted C₆-C₁₀ arylene, or unsubstituted 5 to9 membered heteroarylene.

In embodiments, ring A is substituted or unsubstituted arylene orsubstituted or unsubstituted heteroarylene. In embodiments, ring A issubstituted or unsubstituted C₆-C₁₀ arylene. In embodiments, ring A isunsubstituted naphthalenyl (i.e. divalent naphthalene moiety). Inembodiments, ring A is substituted naphthalenyl. In embodiments, ring Ais unsubstituted phenylene (divalent benzene moiety or benzene-di-yl).In embodiments, ring A is substituted phenylene (divalent benzene moietyor benzene-di-yl).

In embodiments, ring A is R⁴¹-substituted or unsubstitutedcycloalkylene, R⁴¹-substituted or unsubstituted heterocycloalkylene,R⁴¹-substituted or unsubstituted arylene, or R⁴¹-substituted orunsubstituted heteroarylene. In embodiments, ring A is substituted with1 to 6 optionally different R⁴¹ substituents. In embodiments, ring A issubstituted with 1 R⁴¹ substituent. In embodiments, ring A issubstituted with 2 optionally different R⁴¹ substituents. Inembodiments, ring A is substituted with 3 optionally different R⁴¹substituents. In embodiments, ring A is substituted with 4 optionallydifferent R⁴¹ substituents. In embodiments, ring A is substituted with 5optionally different R⁴¹ substituents. In embodiments, ring A issubstituted with 6 optionally different R⁴¹ substituents.

R⁴¹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴²-substituted or unsubstituted alkyl, R⁴²-substituted or unsubstitutedheteroalkyl, R⁴²-substituted or unsubstituted cycloalkyl,R⁴²-substituted or unsubstituted heterocycloalkyl, R⁴²-substituted orunsubstituted aryl, or R⁴²-substituted or unsubstituted heteroaryl. Inembodiments, R⁴¹ is —OCH₃.

R⁴² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴³-substituted or unsubstituted alkyl, R⁴³-substituted or unsubstitutedheteroalkyl, R⁴³-substituted or unsubstituted cycloalkyl,R⁴³-substituted or unsubstituted heterocycloalkyl, R⁴³-substituted orunsubstituted aryl, or R⁴³-substituted or unsubstituted heteroaryl.

In embodiments, R¹ is hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl, —SOR¹⁰,—SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)m,—NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NRR′, —OR¹⁰, —NR⁷SO_(n)R¹⁰,—NR^(7b)C═(O)R⁹, —NR^(7b)C(O)OR⁹, —NR⁷OR⁹, —OCX^(b) ₃, or —OCHX₂.

In embodiments, R¹ is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R¹ is substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R¹ is hydrogen, substituted alkyl, substituted heteroalkyl,substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl,or substituted heteroaryl. In embodiments, R¹ is hydrogen, unsubstitutedalkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl,unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstitutedheteroaryl. In embodiments, R¹ is hydrogen. In embodiments, R¹ ishydrogen and L² is —NHC(O)—.

In embodiments, R¹ is hydrogen, substituted or unsubstituted C₁-C₈alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl,substituted or unsubstituted C₃-C₈ cycloalkyl, substituted orunsubstituted 3 to 8 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 10membered heteroaryl. In embodiments, R¹ is hydrogen, substituted orunsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2 to 6 memberedheteroalkyl, substituted or unsubstituted C₃-C₆ cycloalkyl, substitutedor unsubstituted 3 to 6 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 9membered heteroaryl.

In embodiments, R¹ is substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R¹ is substituted or unsubstituted aryl or substituted orunsubstituted heteroaryl. In embodiments, R¹ is substituted phenyl. Inembodiments, R¹ is unsubstituted phenyl. In embodiments, R¹ is phenylsubstituted with —CF₃ or halogen. In embodiments, R¹ is phenylmeta-substituted with —CF₃. In embodiments, R¹ is phenylmeta-substituted with —F. In embodiments, R¹ is phenyl meta-substitutedwith —Cl. In embodiments, R¹ is phenyl meta-substituted with —Br. Inembodiments, R¹ is phenyl meta-substituted with —I. In embodiments, R¹is phenyl meta-substituted with —CH₃. In embodiments, R¹ is —OPh,—CH₂Ph, —OCH₂Ph, —NHC(O)H, or —CHO. In embodiments, R¹ is phenylmeta-substituted with —CCl₃. In embodiments, R¹ is phenylpara-substituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph,or —CHO. In embodiments, R¹ is phenyl meta-substituted with —CF₃, —Cl,—OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph, or —CHO. In embodiments, R¹ isphenyl ortho-substituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh,—CH₂Ph, or —CHO. In embodiments, R¹ is aryl meta-substituted with —CF₃,—Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph, or —CHO. In embodiments, R¹is aryl ortho-substituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh,—CH₂Ph, or —CHO. In embodiments, R¹ is aryl para-substituted with —CF₃,—Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph, or —CHO. In embodiments, R¹is aryl substituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh,—CH₂Ph, or —CHO. In embodiments, R¹ is heteroaryl substituted with —CF₃,—Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph, or —CHO. In embodiments, R¹is phenyl substituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh,—CH₂Ph, or —CHO. In embodiments, R¹ is 5 to 6 membered heteroarylsubstituted with —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh, —CH₂Ph, or—CHO. In embodiments, R¹ is unsubstituted cyclohexyl. In embodiments, R¹is substituted cyclohexyl. In embodiments, R¹ is unsubstitutedcyclopenyl. In embodiments, R¹ is substituted cyclopenyl. Inembodiments, R¹ is unsubstituted cyclobutyl. In embodiments, R¹ issubstituted cyclobutyl. In embodiments, R¹ is unsubstituted cyclopropyl.In embodiments, R¹ is substituted cyclopropyl.

In embodiments, R¹ is a substituted or unsubstituted heteroaryl selectedfrom the group consisting of pyridinyl, pyrimidinyl, thiophenyl,thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl,benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl,quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl,imidazopyridinyl, benzofuranyl, benzothienyl, benzothiophenyl, phenyl,naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl,oxazolyl, isoxazolyl, thiazolyl, furylthienyl, pyridyl, pyrimidyl,benzothiazolyl, purinyl, benzimidazolyl, isoquinolyl, thiadiazolyl,oxadiazolyl, pyrrolyl, diazolyl, triazolyl, tetrazolyl,benzothiadiazolyl, isothiazolyl, pyrazolopyrimidinyl,pyrrolopyrimidinyl, benzotriazolyl, benzoxazolyl, and quinolyl.

In some embodiments of the compounds provided herein, R¹ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹⁵-substituted or unsubstituted alkyl, R¹¹-substituted or unsubstitutedheteroalkyl, R¹⁵-substituted or unsubstituted cycloalkyl,R¹¹-substituted or unsubstituted heterocycloalkyl, R¹⁵-substituted orunsubstituted aryl, or R¹¹-substituted or unsubstituted heteroaryl. Inembodiments, R¹ is substituted with 1 to 6 optionally different R¹¹substituents. In embodiments, R¹ is substituted with 1 R¹¹ substituent.In embodiments, R¹ is substituted with 2 optionally different R¹¹substituents. In embodiments, R¹ is substituted with 3 optionallydifferent R¹¹ substituents. In embodiments, R¹ is substituted with 4optionally different R¹¹ substituents. In embodiments, R¹ is substitutedwith 5 optionally different R¹¹ substituents. In embodiments, R¹ issubstituted with 6 optionally different R¹¹ substituents. Inembodiments, R¹ is substituted with 7 optionally different R¹¹substituents. In embodiments, R¹ is phenyl substituted with 1 to 5optionally different R¹¹ substituents. In embodiments, R¹ is phenylsubstituted with 1 R¹¹ substituent. In embodiments, R¹ is phenylsubstituted with 2 optionally different R¹¹ substituents. Inembodiments, R¹ is phenyl substituted with 3 optionally different R¹¹substituents. In embodiments, R¹ is phenyl substituted with 4 optionallydifferent R¹¹ substituents. In embodiments, R¹ is phenyl substitutedwith 5 optionally different R¹¹ substituents. In embodiments, R¹ is arylsubstituted with 1 to 6 optionally different R¹¹ substituents. Inembodiments, R¹ is aryl substituted with 1 R¹¹ substituent. Inembodiments, R¹ is aryl substituted with 2 optionally different R¹¹substituents. In embodiments, R¹ is aryl substituted with 3 optionallydifferent R¹¹ substituents. In embodiments, R¹ is aryl substituted with4 optionally different R¹¹ substituents. In embodiments, R¹ is arylsubstituted with 5 optionally different R¹¹ substituents. Inembodiments, R¹ is aryl substituted with 6 optionally different R¹¹substituents. In embodiments, R¹ is aryl substituted with 7 optionallydifferent R¹¹ substituents. In embodiments, R¹ is heteroaryl substitutedwith 1 to 6 optionally different R¹¹ substituents. In embodiments, R¹ isheteroaryl substituted with 1 R¹¹ substituent. In embodiments, R¹ isheteroaryl substituted with 2 optionally different R¹¹ substituents. Inembodiments, R¹ is heteroaryl substituted with 3 optionally differentR¹¹ substituents. In embodiments, R¹ is heteroaryl substituted with 4optionally different R¹¹ substituents. In embodiments, R¹ is heteroarylsubstituted with 5 optionally different R¹¹ substituents. Inembodiments, R¹ is heteroaryl substituted with 6 optionally differentR¹¹ substituents. In embodiments, R¹ is heteroaryl substituted with 7optionally different R¹¹ substituents.

R¹¹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹²-substituted or unsubstituted alkyl, R¹²-substituted or unsubstitutedheteroalkyl, R¹²-substituted or unsubstituted cycloalkyl,R¹²-substituted or unsubstituted heterocycloalkyl, R¹²-substituted orunsubstituted aryl, or R²-substituted or unsubstituted heteroaryl. Inembodiments, R¹¹ is —CCl₃, —CF₃, —Cl, —OCF₃, —CH₃, —F, —OCH₃, —OPh,—CH₂Ph, or —CHO.

R¹² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹³-substituted or unsubstituted alkyl, R¹³-substituted or unsubstitutedheteroalkyl, R¹³-substituted or unsubstituted cycloalkyl,R¹³-substituted or unsubstituted heterocycloalkyl, R¹³-substituted orunsubstituted aryl, or R¹³-substituted or unsubstituted heteroaryl.

In embodiments, R² is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R² is hydrogen, substituted alkyl, substituted heteroalkyl,substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl,or substituted heteroaryl. In embodiments, R² is hydrogen, unsubstitutedalkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl,unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstitutedheteroaryl.

In embodiments, R² is hydrogen, substituted or unsubstituted C₁-C₈alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl,substituted or unsubstituted C₃-C₈ cycloalkyl, substituted orunsubstituted 3 to 8 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 10membered heteroaryl. In embodiments, R² is hydrogen, substituted orunsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2 to 6 memberedheteroalkyl, substituted or unsubstituted C₃-C₆ cycloalkyl, substitutedor unsubstituted 3 to 6 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 9membered heteroaryl.

In embodiments, R² is substituted or unsubstituted alkyl. Inembodiments, R² is substituted or unsubstituted C₁-C₆ alkyl. Inembodiments, R² is unsubstituted C₁-C₆ alkyl. In embodiments, R² isunsubstituted methyl. In embodiments, R² is unsubstituted isopropyl. Inembodiments, R² is unsubstituted ethyl. In embodiments, R² isunsubstituted propyl (e.g. n-propyl or isopropyl). In embodiments, R² isunsubstituted isopropyl. In embodiments, R² is unsubstituted butyl (e.g.n-butyl, sec-butyl, isobutyl, or tert-butyl). In embodiments, R² isunsubstituted tert-butyl. In embodiments, R² is unsubstituted iso-butyl.In embodiments, R² is unsubstituted pentyl (e.g. n-pentyl, tert-pentyl,neopentyl, isopentyl, sec-pentyl, or 3-pentyl). In embodiments, R² isunsubstituted cyclopropyl. In embodiments, R² is unsubstitutedcyclobutyl. In embodiments, R² is unsubstituted cyclopentyl. Inembodiments, R² is unsubstituted cyclohexyl.

In some embodiments, R² is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R¹⁴-substituted or unsubstitutedalkyl, R¹⁴-substituted or unsubstituted heteroalkyl, R¹⁴-substituted orunsubstituted cycloalkyl, R¹⁴-substituted or unsubstitutedheterocycloalkyl, R¹⁴-substituted or unsubstituted aryl, orR¹⁴-substituted or unsubstituted heteroaryl.

R¹⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹⁵-substituted or unsubstituted alkyl, R¹⁵-substituted or unsubstitutedheteroalkyl, R¹⁵-substituted or unsubstituted cycloalkyl, Ri-substitutedor unsubstituted heterocycloalkyl, R¹⁵-substituted or unsubstitutedaryl, or Ri-substituted or unsubstituted heteroaryl.

R¹⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹⁶-substituted or unsubstituted alkyl, R¹⁶-substituted or unsubstitutedheteroalkyl, R¹⁶-substituted or unsubstituted cycloalkyl,R¹⁶-substituted or unsubstituted heterocycloalkyl, R¹⁶-substituted orunsubstituted aryl, or R¹⁶-substituted or unsubstituted heteroaryl.

In embodiments, R³ is independently hydrogen, oxo, halogen, —CX^(b) ₃,—CN, —SO₂Cl, —SO_(n2)R^(10b), —SO_(v2)NR^(7b)R^(8b), —NHNH₂,—ONR^(7b)R^(8b), —NHC═(O)NHNH₂, —NHC═(O)NR^(7b)R^(8b), —N(O)_(m2),—NR^(7b)R^(8b), —C(O)R^(9b), —C(O)—OR^(9b), —C(O)NR^(7b)R^(8b),—OR^(10b), —NR^(7b)SO_(n2)R^(10b), —NR^(7b)C═(O)R^(9b),—NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —OCX^(b) ₃, or —OCHX^(b) ₂. Inembodiments, R³ is independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl. In embodiments, R³ is independently hydrogen, substitutedalkyl, substituted heteroalkyl, substituted cycloalkyl, substitutedheterocycloalkyl, substituted aryl, or substituted heteroaryl. Inembodiments, R³ is independently hydrogen, unsubstituted alkyl,unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstitutedheterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In embodiments, R³ is independently hydrogen, substituted orunsubstituted C₁-C₈ alkyl, substituted or unsubstituted 2 to 8 memberedheteroalkyl, substituted or unsubstituted C₃-C₈ cycloalkyl, substitutedor unsubstituted 3 to 8 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 10membered heteroaryl. In embodiments, R³ is independently hydrogen,substituted or unsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2to 6 membered heteroalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted 3 to 6 memberedheterocycloalkyl, substituted or unsubstituted C₆-C₁₀ aryl, orsubstituted or unsubstituted 5 to 9 membered heteroaryl.

In embodiments, R³ is independently hydrogen, halogen, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. In embodiments, R³ is independently hydrogen.In embodiments, R³ is independently halogen.

In some embodiments, R³ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R¹⁷-substituted or unsubstitutedalkyl, R¹⁷-substituted or unsubstituted heteroalkyl, R¹⁷-substituted orunsubstituted cycloalkyl, R¹⁷-substituted or unsubstitutedheterocycloalkyl, R¹⁷-substituted or unsubstituted aryl, orR¹⁷-substituted or unsubstituted heteroaryl.

R¹⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹⁸-substituted or unsubstituted alkyl, R¹⁸-substituted or unsubstitutedheteroalkyl, R¹⁸-substituted or unsubstituted cycloalkyl,R¹⁸-substituted or unsubstituted heterocycloalkyl, R¹⁸-substituted orunsubstituted aryl, or R¹⁸-substituted or unsubstituted heteroaryl.

R¹⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R¹⁹-substituted or unsubstituted alkyl, R¹⁹-substituted or unsubstitutedheteroalkyl, R¹⁹-substituted or unsubstituted cycloalkyl,R¹⁹-substituted or unsubstituted heterocycloalkyl, R¹⁹-substituted orunsubstituted aryl, or R¹⁹-substituted or unsubstituted heteroaryl.

In embodiments, R⁴ and R⁵ are independently hydrogen. In embodiments, R⁴and R⁵ are independently unsubstituted C₁-C₆ alkyl. In embodiments, R⁴and R⁵ are independently unsubstituted C₁-C₅ alkyl. In embodiments, R⁴and R⁵ are independently unsubstituted C₁-C₄ alkyl. In embodiments, R⁴and R⁵ are independently unsubstituted C₁-C₃ alkyl. In embodiments, R⁴and R⁵ are independently unsubstituted C₁-C₂ alkyl. In embodiments, R⁴and R⁵ are independently unsubstituted methyl.

In embodiments, L¹ is a bond. In embodiments, L¹ is unsubstituted C₁-C₅alkylene. In embodiments, L¹ is unsubstituted C₁-C₄ alkylene. Inembodiments, L¹ is unsubstituted C₁-C₃ alkylene. In embodiments, L¹ isunsubstituted C₁-C₂ alkylene. In embodiments, L¹ is unsubstitutedmethylene.

In embodiments, L² is a bond. In embodiments, L² is —NR^(6a)—. Inembodiments, L² is —O—. In embodiments, L² is —S—. In embodiments, L² is—C(O)—. In embodiments, L² is —S(O)—. In embodiments, L² is —S(O)₂—. Inembodiments, L² is —C(O)(CH₂)_(z2)—. In embodiments, L² is—NR^(6a)C(O)—. In embodiments, L² is —C(O)NR^(6b)—. In embodiments, L²is —NR^(6a)C(O)O—. In embodiments, L² is —NR^(6a)C(O)NR^(6b). Inembodiments, L² is —NH—. In embodiments, L² is —NHC(O)—. In embodiments,L² is —C(O)NH—. In embodiments, L² is —NHC(O)NH—. In embodiments, L² is—NHC(O)OCH₂—. In embodiments, L² is substituted or unsubstitutedalkylene, substituted or unsubstituted heteroalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene. In embodiments, L² is—C(O)(CH₂)—. In embodiments, L² is —C(O)(CH₂)₂—. In embodiments, L² is—C(O)(CH₂)₃—. In embodiments, L² is —C(O)(CH₂)₄—.

In embodiments, L² is substituted or unsubstituted alkylene, substitutedor unsubstituted heteroalkylene, substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, or substituted or unsubstitutedheteroarylene. In embodiments, L² is substituted alkylene, substitutedheteroalkylene, substituted cycloalkylene, substitutedheterocycloalkylene, substituted arylene, or substituted heteroarylene.In embodiments, L² is unsubstituted alkylene, unsubstitutedheteroalkylene, unsubstituted cycloalkylene, unsubstitutedheterocycloalkylene, unsubstituted arylene, or unsubstitutedheteroarylene.

In embodiments, L² is substituted or unsubstituted C₁-C₈ alkylene,substituted or unsubstituted 2 to 8 membered heteroalkylene, substitutedor unsubstituted C₃-C₈ cycloalkylene, substituted or unsubstituted 3 to8 membered heterocycloalkylene, substituted or unsubstituted C₆-C₁₀arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.In embodiments, L² is substituted or unsubstituted C₁-C₆ alkylene,substituted or unsubstituted 2 to 6 membered heteroalkylene, substitutedor unsubstituted C₃-C₆ cycloalkylene, substituted or unsubstituted 3 to6 membered heterocycloalkylene, substituted or unsubstituted C₆-C₁₀arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.

In some embodiments, L² is independently R⁴⁴-substituted orunsubstituted alkylene, R⁴⁴-substituted or unsubstituted heteroalkylene,R⁴⁴-substituted or unsubstituted cycloalkylene, R⁴⁴-substituted orunsubstituted heterocycloalkylene, R⁴⁴-substituted or unsubstitutedarylene, or R⁴⁴-substituted or unsubstituted heteroarylene.

R⁴⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁵-substituted or unsubstituted alkyl, R⁴⁵-substituted or unsubstitutedheteroalkyl, R⁴⁵-substituted or unsubstituted cycloalkyl,R⁴⁵-substituted or unsubstituted heterocycloalkyl, R⁴⁵-substituted orunsubstituted aryl, or R⁴⁵-substituted or unsubstituted heteroaryl.

R⁴⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁶-substituted or unsubstituted alkyl, R⁴⁶-substituted or unsubstitutedheteroalkyl, R⁴⁶-substituted or unsubstituted cycloalkyl,R⁴⁶-substituted or unsubstituted heterocycloalkyl, R⁴⁶-substituted orunsubstituted aryl, or R⁴⁶-substituted or unsubstituted heteroaryl.

In embodiments, R^(6a) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R^(6a) is hydrogen, substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, or substituted heteroaryl. In embodiments, R^(6a) ishydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstitutedcycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, orunsubstituted heteroaryl. In embodiments, R^(6a) is hydrogen. Inembodiments, R^(6a) is unsubstituted methyl. In embodiments, R^(6a) isunsubstituted ethyl. In embodiments, R^(6a) is unsubstituted propyl.

In embodiments, R^(6a) is hydrogen, substituted or unsubstituted C₁-C₈alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl,substituted or unsubstituted C₃-C₈ cycloalkyl, substituted orunsubstituted 3 to 8 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 10membered heteroaryl. In embodiments, R^(6a) is hydrogen, substituted orunsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2 to 6 memberedheteroalkyl, substituted or unsubstituted C₃-C₆ cycloalkyl, substitutedor unsubstituted 3 to 6 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 9membered heteroaryl.

In some embodiments of the compounds provided herein, R^(6a) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —S₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(26a)-substituted or unsubstituted alkyl, R^(26a)-substituted orunsubstituted heteroalkyl, R^(26a)-substituted or unsubstitutedcycloalkyl, R^(26a)-substituted or unsubstituted heterocycloalkyl,R^(26a)-substituted or unsubstituted aryl, or R^(26a)-substituted orunsubstituted heteroaryl.

R^(26a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(27a)-substituted or unsubstituted alkyl,R^(27a)-substituted or unsubstituted heteroalkyl, R^(27a)-substituted orunsubstituted cycloalkyl, R^(27a)-substituted or unsubstitutedheterocycloalkyl, R^(27a)-substituted or unsubstituted aryl, orR^(27a)-substituted or unsubstituted heteroaryl.

R^(27a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(28a)-substituted or unsubstituted alkyl,R^(28a)-substituted or unsubstituted heteroalkyl, R^(28a)-substituted orunsubstituted cycloalkyl, R^(28a)-substituted or unsubstitutedheterocycloalkyl, R^(28a)-substituted or unsubstituted aryl, orR^(28a)-substituted or unsubstituted heteroaryl.

In embodiments, R^(6b) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, R^(6b) is hydrogen, substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, or substituted heteroaryl. In embodiments, R^(6b) ishydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstitutedcycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, orunsubstituted heteroaryl. In embodiments, R^(6b) is hydrogen. Inembodiments, R^(6b) is unsubstituted methyl. In embodiments, R^(6b) isunsubstituted ethyl. In embodiments, R^(6b) is unsubstituted propyl.

In embodiments, R^(6b) is hydrogen, substituted or unsubstituted C₁-C₈alkyl, substituted or unsubstituted 2 to 8 membered heteroalkyl,substituted or unsubstituted C₃-C₈ cycloalkyl, substituted orunsubstituted 3 to 8 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 10membered heteroaryl. In embodiments, R^(6b) is hydrogen, substituted orunsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2 to 6 memberedheteroalkyl, substituted or unsubstituted C₃-C₆ cycloalkyl, substitutedor unsubstituted 3 to 6 membered heterocycloalkyl, substituted orunsubstituted C₆-C₁₀ aryl, or substituted or unsubstituted 5 to 9membered heteroaryl.

In some embodiments of the compounds provided herein, R^(6b) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(26b)-substituted or unsubstituted alkyl, R^(26b)-substituted orunsubstituted heteroalkyl, R^(26b)-substituted or unsubstitutedcycloalkyl, R^(26b)-substituted or unsubstituted heterocycloalkyl,R^(26b)-substituted or unsubstituted aryl, or R^(26b)-substituted orunsubstituted heteroaryl.

R^(26b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(27b)-substituted or unsubstituted alkyl,R^(27b)-substituted or unsubstituted heteroalkyl, R^(27b)-substituted orunsubstituted cycloalkyl, R^(27b)-substituted or unsubstitutedheterocycloalkyl, R^(27b)-substituted or unsubstituted aryl, orR^(27b)-substituted or unsubstituted heteroaryl.

R^(27b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(21b)-substituted or unsubstituted alkyl,R^(28b)-substituted or unsubstituted heteroalkyl, R^(28b)-substituted orunsubstituted cycloalkyl, R^(28b)-substituted or unsubstitutedheterocycloalkyl, R^(28b)-substituted or unsubstituted aryl, orR^(28b)-substituted or unsubstituted heteroaryl.

In embodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a), R^(8a), R^(9a), R^(10a),is independently hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Inembodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a), R^(8a), R^(9a), R^(10a),R^(7b), R^(8b), R^(9b) and R^(10b) is independently hydrogen,substituted alkyl, substituted heteroalkyl, substituted cycloalkyl,substituted heterocycloalkyl, substituted aryl, or substitutedheteroaryl. In embodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a), R^(8a),R^(9a), R^(10a), R^(7b), R^(8b), R^(9b) and R^(10b) is independentlyhydrogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstitutedcycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, orunsubstituted heteroaryl. In embodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a),R^(8a), R^(9a), R^(10a), R^(7b), R^(8b), R^(9b) and R^(10b) isindependently hydrogen.

In embodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a), R^(8a), R^(9a), R^(10a),R^(10b), R^(8b), R^(9b) and R^(10b) is independently hydrogen,substituted or unsubstituted C₁-C₈ alkyl, substituted or unsubstituted 2to 8 membered heteroalkyl, substituted or unsubstituted C₃-C₈cycloalkyl, substituted or unsubstituted 3 to 8 memberedheterocycloalkyl, substituted or unsubstituted C₆-C₁₀ aryl, orsubstituted or unsubstituted 5 to 10 membered heteroaryl. Inembodiments, each R⁷, R⁸, R⁹, R¹⁰, R^(7a), R^(8a), R^(9a), R^(10a),R^(7b), R^(8b), R^(9b) and R^(10b) is independently hydrogen,substituted or unsubstituted C₁-C₆ alkyl, substituted or unsubstituted 2to 6 membered heteroalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted 3 to 6 memberedheterocycloalkyl, substituted or unsubstituted C₆-C₁₀ aryl, orsubstituted or unsubstituted 5 to 9 membered heteroaryl.

In some embodiments, R⁷ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —S₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R²⁹-substituted or unsubstitutedalkyl, R²⁹-substituted or unsubstituted heteroalkyl, R²⁹-substituted orunsubstituted cycloalkyl, R²⁹-substituted or unsubstitutedheterocycloalkyl, R²⁹-substituted or unsubstituted aryl, orR²⁹-substituted or unsubstituted heteroaryl. In embodiments, R⁷ and R⁸substituents bonded to the same nitrogen atom may be joined to form anR²⁹-substituted or unsubstituted heterocycloalkyl or R²⁹-substituted orunsubstituted heteroaryl.

R²⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁰-substituted or unsubstituted alkyl, R³⁰-substituted or unsubstitutedheteroalkyl, R³⁰-substituted or unsubstituted cycloalkyl,R³⁰-substituted or unsubstituted heterocycloalkyl, R³⁰-substituted orunsubstituted aryl, or R³⁰-substituted or unsubstituted heteroaryl.

R³⁰ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³¹-substituted or unsubstituted alkyl, R³¹-substituted or unsubstitutedheteroalkyl, R³¹-substituted or unsubstituted cycloalkyl,R³¹-substituted or unsubstituted heterocycloalkyl, R³¹-substituted orunsubstituted aryl, or R³¹-substituted or unsubstituted heteroaryl.

In some embodiments, R⁷ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(29a)-substituted or unsubstitutedalkyl, R^(29a)-substituted or unsubstituted heteroalkyl,R^(29a)-substituted or unsubstituted cycloalkyl, R^(29a)-substituted orunsubstituted heterocycloalkyl, R^(29a)-substituted or unsubstitutedaryl, or R^(29a)-substituted or unsubstituted heteroaryl. Inembodiments, R^(7a) and R^(a) substituents bonded to the same nitrogenatom may be joined to form an R^(29a)-substituted or unsubstitutedheterocycloalkyl or R^(29a)-substituted or unsubstituted heteroaryl.

R^(29a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(30a)-substituted or unsubstituted alkyl,R^(30a)-substituted or unsubstituted heteroalkyl, R^(30a)-substituted orunsubstituted cycloalkyl, R^(30a)-substituted or unsubstitutedheterocycloalkyl, R^(30a)-substituted or unsubstituted aryl, orR^(30a)-substituted or unsubstituted heteroaryl.

R^(30a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(31a)-substituted or unsubstituted alkyl,R^(31a)-substituted or unsubstituted heteroalkyl, R^(31a)-substituted orunsubstituted cycloalkyl, R^(31a)-substituted or unsubstitutedheterocycloalkyl, R^(31a)-substituted or unsubstituted aryl, orR^(31a)-substituted or unsubstituted heteroaryl.

In some embodiments, R^(7b) is independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H, —SO₄H, —S₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(29b)-substituted or unsubstitutedalkyl, R^(29b)-substituted or unsubstituted heteroalkyl,R^(29b)-substituted or unsubstituted cycloalkyl, R^(29b)-substituted orunsubstituted heterocycloalkyl, R^(29b)-substituted or unsubstitutedaryl, or R^(29b)-substituted or unsubstituted heteroaryl. Inembodiments, R^(7b) and R^(8b) substituents bonded to the same nitrogenatom may be joined to form an R^(29b)-substituted or unsubstitutedheterocycloalkyl or R^(29b)-substituted or unsubstituted heteroaryl.

R^(29b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(3b)-substituted or unsubstituted alkyl,R^(30b)-substituted or unsubstituted heteroalkyl, R^(30b)-substituted orunsubstituted cycloalkyl, R^(30b)-substituted or unsubstitutedheterocycloalkyl, R^(30b)-substituted or unsubstituted aryl, orR^(30b)-substituted or unsubstituted heteroaryl.

R^(30b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(3b)-substituted or unsubstituted alkyl,R^(31b)-substituted or unsubstituted heteroalkyl, R^(31b)-substituted orunsubstituted cycloalkyl, R^(31b)-substituted or unsubstitutedheterocycloalkyl, R^(31b)-substituted or unsubstituted aryl, orR^(3b)-substituted or unsubstituted heteroaryl.

In some embodiments, R⁸ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R³²-substituted or unsubstitutedalkyl, R³²-substituted or unsubstituted heteroalkyl, R³²-substituted orunsubstituted cycloalkyl, R³²-substituted or unsubstitutedheterocycloalkyl, R³²-substituted or unsubstituted aryl, orR³²-substituted or unsubstituted heteroaryl. In embodiments, R⁷ and R⁸substituents bonded to the same nitrogen atom may be joined to form anR³²-substituted or unsubstituted heterocycloalkyl or R³²-substituted orunsubstituted heteroaryl.

R³² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³³-substituted or unsubstituted alkyl, R³³-substituted or unsubstitutedheteroalkyl, R³³-substituted or unsubstituted cycloalkyl,R³³-substituted or unsubstituted heterocycloalkyl, R³³-substituted orunsubstituted aryl, or R³³-substituted or unsubstituted heteroaryl.

R³³ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁴-substituted or unsubstituted alkyl, R³⁴-substituted or unsubstitutedheteroalkyl, R³⁴-substituted or unsubstituted cycloalkyl,R³⁴-substituted or unsubstituted heterocycloalkyl, R³⁴-substituted orunsubstituted aryl, or R³⁴-substituted or unsubstituted heteroaryl.

In some embodiments, R^(8a) is independently hydrogen,

halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(32a)-substituted orunsubstituted alkyl, R^(32a)-substituted or unsubstituted heteroalkyl,R^(32a)-substituted or unsubstituted cycloalkyl, R^(32a)-substituted orunsubstituted heterocycloalkyl, R^(32a)-substituted or unsubstitutedaryl, or R^(32a)-substituted or unsubstituted heteroaryl. Inembodiments, R^(7a) and R^(8a) substituents bonded to the same nitrogenatom may be joined to form an R^(32a)-substituted or unsubstitutedheterocycloalkyl or R^(32a)-substituted or unsubstituted heteroaryl.

R^(32a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(33a)-substituted or unsubstituted alkyl,R^(33a)-substituted or unsubstituted heteroalkyl, R^(33a)-substituted orunsubstituted cycloalkyl, R^(33a)-substituted or unsubstitutedheterocycloalkyl, R^(33a)-substituted or unsubstituted aryl, orR^(33a)-substituted or unsubstituted heteroaryl.

R^(33a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(34a)-substituted or unsubstituted alkyl,R^(34a)-substituted or unsubstituted heteroalkyl, R^(34a)-substituted orunsubstituted cycloalkyl, R^(34a)-substituted or unsubstitutedheterocycloalkyl, R^(34a)-substituted or unsubstituted aryl, orR^(34a)-substituted or unsubstituted heteroaryl.

In some embodiments, R^(8b) is independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H, —SO₄H, —S₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(32b)-substituted or unsubstitutedalkyl, R^(32b)-substituted or unsubstituted heteroalkyl,R^(32b)-substituted or unsubstituted cycloalkyl, R^(32b)-substituted orunsubstituted heterocycloalkyl, R^(32b)-substituted or unsubstitutedaryl, or R^(32b)-substituted or unsubstituted heteroaryl. Inembodiments, R^(7b) and R^(8b) substituents bonded to the same nitrogenatom may be joined to form an R^(32b)-substituted or unsubstitutedheterocycloalkyl or R^(32b)-substituted or unsubstituted heteroaryl.

R^(32b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(33b)-substituted or unsubstituted alkyl,R^(33b)-substituted or unsubstituted heteroalkyl, R^(33b)-substituted orunsubstituted cycloalkyl, R^(33b)-substituted or unsubstitutedheterocycloalkyl, R^(33b)-substituted or unsubstituted aryl, orR^(33b)-substituted or unsubstituted heteroaryl.

R^(33b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(34b)-substituted or unsubstituted alkyl,R^(34b)-substituted or unsubstituted heteroalkyl, R^(34b)-substituted orunsubstituted cycloalkyl, R^(34b)-substituted or unsubstitutedheterocycloalkyl, R^(34b)-substituted or unsubstituted aryl, orR^(34b)-substituted or unsubstituted heteroaryl.

In some embodiments, R⁹ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R³⁵-substituted or unsubstitutedalkyl, R³⁵-substituted or unsubstituted heteroalkyl, R³⁵-substituted orunsubstituted cycloalkyl, R³⁵-substituted or unsubstitutedheterocycloalkyl, R³⁵-substituted or unsubstituted aryl, orR³⁵-substituted or unsubstituted heteroaryl.

R³⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁶-substituted or unsubstituted alkyl, R³⁶-substituted or unsubstitutedheteroalkyl, R³⁶-substituted or unsubstituted cycloalkyl,R³⁶-substituted or unsubstituted heterocycloalkyl, R³⁶-substituted orunsubstituted aryl, or R³⁶-substituted or unsubstituted heteroaryl.

R³⁶ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁷-substituted or unsubstituted alkyl, R³⁷-substituted or unsubstitutedheteroalkyl, R³⁷-substituted or unsubstituted cycloalkyl,R³⁷-substituted or unsubstituted heterocycloalkyl, R³⁷-substituted orunsubstituted aryl, or R³⁷-substituted or unsubstituted heteroaryl.

In some embodiments, R⁹ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(35a)-substituted or unsubstitutedalkyl, R^(35a)-substituted or unsubstituted heteroalkyl,R^(35a)-substituted or unsubstituted cycloalkyl, R^(35a)-substituted orunsubstituted heterocycloalkyl, R^(35a)-substituted or unsubstitutedaryl, or R^(35a)-substituted or unsubstituted heteroaryl.

R^(35a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(36a)-substituted or unsubstituted alkyl,R^(36a)-substituted or unsubstituted heteroalkyl, R^(36a)-substituted orunsubstituted cycloalkyl, R^(36a)-substituted or unsubstitutedheterocycloalkyl, R^(36a)-substituted or unsubstituted aryl, orR^(36a)-substituted or unsubstituted heteroaryl.

R^(36a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(37a)-substituted or unsubstituted alkyl,R^(37a)-substituted or unsubstituted heteroalkyl, R^(37a)-substituted orunsubstituted cycloalkyl, R^(37a)-substituted or unsubstitutedheterocycloalkyl, R^(37a)-substituted or unsubstituted aryl, orR^(37a)-substituted or unsubstituted heteroaryl.

In some embodiments, R^(9b) is independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H, —SO₄H, —S₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(35b)-substituted or unsubstitutedalkyl, R^(35b)-substituted or unsubstituted heteroalkyl,R^(35b)-substituted or unsubstituted cycloalkyl, R^(35b)-substituted orunsubstituted heterocycloalkyl, R^(35b)-substituted or unsubstitutedaryl, or R^(35b)-substituted or unsubstituted heteroaryl.

R^(35b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(36b)-substituted or unsubstituted alkyl,R^(36b)-substituted or unsubstituted heteroalkyl, R^(36b)-substituted orunsubstituted cycloalkyl, R^(36b)-substituted or unsubstitutedheterocycloalkyl, R^(36b)-substituted or unsubstituted aryl, orR^(36b)-substituted or unsubstituted heteroaryl.

R^(36b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(37b)-substituted or unsubstituted alkyl,R^(37b)-substituted or unsubstituted heteroalkyl, R^(37b)-substituted orunsubstituted cycloalkyl, R^(37b)-substituted or unsubstitutedheterocycloalkyl, R^(37b)-substituted or unsubstituted aryl, orR^(37b)-substituted or unsubstituted heteroaryl.

In some embodiments, R¹⁰ is independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R³⁸-substituted or unsubstitutedalkyl, R³⁸-substituted or unsubstituted heteroalkyl, R³⁸-substituted orunsubstituted cycloalkyl, R³⁸-substituted or unsubstitutedheterocycloalkyl, R³⁸-substituted or unsubstituted aryl, orR³⁸-substituted or unsubstituted heteroaryl.

R³⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁹-substituted or unsubstituted alkyl, R³⁹-substituted or unsubstitutedheteroalkyl, R³⁹-substituted or unsubstituted cycloalkyl,R³⁹-substituted or unsubstituted heterocycloalkyl, R³⁹-substituted orunsubstituted aryl, or R³⁹-substituted or unsubstituted heteroaryl.

R³⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁰-substituted or unsubstituted alkyl, R⁴⁰-substituted or unsubstitutedheteroalkyl, R⁴⁰-substituted or unsubstituted cycloalkyl,R⁴⁰-substituted or unsubstituted heterocycloalkyl, R⁴⁰-substituted orunsubstituted aryl, or R⁴⁰-substituted or unsubstituted heteroaryl.

In some embodiments, R^(10a) is independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(38a)-substituted or unsubstitutedalkyl, R^(38a)-substituted or unsubstituted heteroalkyl,R^(38a)-substituted or unsubstituted cycloalkyl, R^(38a)-substituted orunsubstituted heterocycloalkyl, R^(38a)-substituted or unsubstitutedaryl, or R^(38a)-substituted or unsubstituted heteroaryl.

R^(38a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(39a)-substituted or unsubstituted alkyl,R^(39a)-substituted or unsubstituted heteroalkyl, R^(39a)-substituted orunsubstituted cycloalkyl, R^(39a)-substituted or unsubstitutedheterocycloalkyl, R^(39a)-substituted or unsubstituted aryl, orR^(39a)-substituted or unsubstituted heteroaryl.

R^(39a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(40a)-substituted or unsubstituted alkyl,R^(40a)-substituted or unsubstituted heteroalkyl, R^(40a)-substituted orunsubstituted cycloalkyl, R^(40a)-substituted or unsubstitutedheterocycloalkyl, R^(40a)-substituted or unsubstituted aryl, orR^(40a)-substituted or unsubstituted heteroaryl.

In some embodiments, R^(10b) is independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —S₃H, —SO₄H, —S₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, R^(38b)-substituted or unsubstitutedalkyl, R^(38b)-substituted or unsubstituted heteroalkyl,R^(38b)-substituted or unsubstituted cycloalkyl, R^(38b)-substituted orunsubstituted heterocycloalkyl, R^(38b)-substituted or unsubstitutedaryl, or R^(38b)-substituted or unsubstituted heteroaryl.

R^(38b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(39b)-substituted or unsubstituted alkyl,R^(39b)-substituted or unsubstituted heteroalkyl, R^(39b)-substituted orunsubstituted cycloalkyl, R^(39b)-substituted or unsubstitutedheterocycloalkyl, R^(39b)-substituted or unsubstituted aryl, orR^(39b)-substituted or unsubstituted heteroaryl.

R^(39b) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(4b)-substituted or unsubstituted alkyl,R^(40b)-substituted or unsubstituted heteroalkyl, R^(40b)-substituted orunsubstituted cycloalkyl, R^(40b)-substituted or unsubstitutedheterocycloalkyl, R^(40b)-substituted or unsubstituted aryl, orR^(40b)-substituted or unsubstituted heteroaryl.

In embodiments, v is 1. In embodiments, v is 2. In embodiments, v1 is 1.In embodiments, v1 is 2. In embodiments, v2 is 1. In embodiments, v2 is2. In embodiments, m is 1. In embodiments, m is 2. In embodiments, m1is 1. In embodiments, m1 is 2. In embodiments, m2 is 1. In embodiments,m2 is 2. In embodiments, n is independently 0. In embodiments, n isindependently 1. In embodiments, n is independently 2. In embodiments, nis independently 3. In embodiments, n is independently 4. Inembodiments, n1 is independently 0. In embodiments, n1 isindependently 1. In embodiments, n1 is independently 2. In embodiments,n1 is independently 3. In embodiments, n1 is independently 4. Inembodiments, n2 is independently 0. In embodiments, n2 isindependently 1. In embodiments, n2 is independently 2. In embodiments,n2 is independently 3. In embodiments, n2 is independently 4. Inembodiments, X is —Cl. In embodiments, X is —Br. In embodiments, X is—I. In embodiments, X is —F. In embodiments, X^(a) is —Cl. Inembodiments, X^(a) is —Br. In embodiments, X^(a) is —I. In embodiments,X^(a) is —F. In embodiments, X^(b) is —Cl. In embodiments, X^(b) is —Br.In embodiments, X^(b) is —I. In embodiments, X^(b) is —F. Inembodiments, z is 0. In embodiments, z is 1. In embodiments, z is 2. Inembodiments, z2 is 1. In embodiments, z2 is 2. In embodiments, z2 is 3.In embodiments, z2 is 4.

In embodiments, the compound has the formula:

wherein, R¹, R², R³, R⁴, R⁵, R^(6a), L¹, ring A and z are as describedherein (e.g. compounds of formula I, including embodiments).

L³ is a bond, —O—, —NR^(6b)—, substituted or unsubstituted alkylene,substituted or unsubstituted heteroalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene.

In embodiments, L³ is a bond. In embodiments, L³ is —NR^(6b)—, whereinR^(6b) is as defined herein including embodiments thereof. Inembodiments, L³ is —NH—. In embodiments, L³ is substituted orunsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene. In embodiments, L³ is —O—.In embodiments, L³ is —OCH₂—.

In embodiments, L³ is substituted or unsubstituted alkylene, substitutedor unsubstituted heteroalkylene, substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, or substituted or unsubstitutedheteroarylene. In embodiments, L³ is substituted alkylene, substitutedheteroalkylene, substituted cycloalkylene, substitutedheterocycloalkylene, substituted arylene, or substituted heteroarylene.In embodiments, L³ is unsubstituted alkylene, unsubstitutedheteroalkylene, unsubstituted cycloalkylene, unsubstitutedheterocycloalkylene, unsubstituted arylene, or unsubstitutedheteroarylene.

In embodiments, L³ is substituted or unsubstituted C₁-C₈ alkylene,substituted or unsubstituted 2 to 8 membered heteroalkylene, substitutedor unsubstituted C₃-C₈ cycloalkylene, substituted or unsubstituted 3 to8 membered heterocycloalkylene, substituted or unsubstituted C₆-C₁₀arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.In embodiments, L³ is substituted or unsubstituted C₁-C₆ alkylene,substituted or unsubstituted 2 to 6 membered heteroalkylene, substitutedor unsubstituted C₃-C₆ cycloalkylene, substituted or unsubstituted 3 to6 membered heterocycloalkylene, substituted or unsubstituted C₆-C₁₀arylene, or substituted or unsubstituted 5 to 9 membered heteroarylene.

In some embodiments, L³ is independently R⁴⁷-substituted orunsubstituted alkylene, R⁴⁷-substituted or unsubstituted heteroalkylene,R⁴⁷-substituted or unsubstituted cycloalkylene, R⁴⁷-substituted orunsubstituted heterocycloalkylene, R⁴⁷-substituted or unsubstitutedarylene, or R⁴⁷-substituted or unsubstituted heteroarylene.

R⁴⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁸-substituted or unsubstituted alkyl, R⁴⁸-substituted or unsubstitutedheteroalkyl, R⁴⁸-substituted or unsubstituted cycloalkyl,R⁴⁸-substituted or unsubstituted heterocycloalkyl, R⁴⁸-substituted orunsubstituted aryl, or R⁴⁸-substituted or unsubstituted heteroaryl.

R⁴⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁹-substituted or unsubstituted alkyl, R⁴⁹-substituted or unsubstitutedheteroalkyl, R⁴⁹-substituted or unsubstituted cycloalkyl,R⁴⁹-substituted or unsubstituted heterocycloalkyl, R⁴⁹-substituted orunsubstituted aryl, or R⁴⁹-substituted or unsubstituted heteroaryl.

Each R¹³, R¹⁶, R¹⁹, R^(28a), R^(28b), R³¹, R^(31a), R^(31b), R³⁴,R^(34a), R^(34b), R³⁷, R^(37a), R^(37b), R⁴, R^(40a), R^(40b), R⁴³, R⁴⁶,and R⁴⁹ is independently a hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, or unsubstituted heteroaryl. In embodiments, each R¹³, R¹⁶, R¹⁹,R^(28a), R^(28b), R³¹, R^(31a), R^(31b), R³⁴, R^(34a), R^(34b), R³⁷,R^(37a), R^(37b), R⁴⁰, R^(40a), R^(40b), R⁴³, R⁴⁶, and R⁴⁹ isindependently hydrogen, unsubstituted C₁-C₅ alkyl, unsubstituted 2 to 8membered heteroalkyl, unsubstituted C₃-C₆ cycloalkyl, unsubstituted 3 to8 membered heterocycloalkyl, unsubstituted C₆-C₁₀ aryl, or unsubstituted5 to 10 membered heteroaryl. In embodiments, each R¹³, R¹⁶, R¹⁹,R^(28a), R^(28b), R³¹, R^(31a), R^(31b), R³⁴, R^(34a), R^(34b), R³⁷,R^(37a), R³⁷, R⁴⁰, R^(40a), R^(40b), R⁴³, R⁴⁶, and R⁴⁹ is independentlyhydrogen, unsubstituted C₁-C₆ alkyl, unsubstituted 2 to 6 memberedheteroalkyl, unsubstituted C₃-C₆ cycloalkyl, unsubstituted 3 to 6membered heterocycloalkyl, unsubstituted C₆-C₁₀ aryl, or unsubstituted 5to 9 membered heteroaryl. In embodiments, each R¹³, R¹⁶, R¹⁹, R^(28a),R^(28b), R³¹, R^(31a), R^(31b), R³⁴, R^(34a), R^(34b), R³⁷, R^(37a),R^(37b), R⁴⁰, R^(40a), R^(40b), R⁴³, R⁴⁶, and R⁴⁹ is hydrogen, oxo,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, or —OCHF₂.

In embodiments, the compound has the formula:

wherein, R¹, R², R³, R^(6a), L³, and ring A are as described herein(e.g. compounds of formula I or II, including embodiments).

In embodiments, the compound is:

In embodiments, the compound is an inhibitor of Ire1. In embodiments,the compound is an inhibitor of Ire1α. In embodiments, the compound isan inhibitor of Ire1α kinase activity. In embodiments, the compound isan inhibitor of Ire1α RNase activity. In embodiments, the compound bindsthe ATP binding site of Ire1α. In embodiments, the compound binds Ire1αin the DFG-out conformation. In embodiments, the compound induces theDFG-out conformation of Ire1α. In embodiments, the compound is aninhibitor of Ire1α oligomerization. In embodiments, the compound is aninhibitor of Ire1α dimerization. In embodiments, the compound is aninhibitor of Ire1α phosphorylation. In embodiments, the compound is aninhibitor of Ire1α autophosphorylation. In embodiments, the compound isan inhibitor of apoptosis. In embodiments, the compound is an inhibitorof Ire1α induced apoptosis. In embodiments, the compound is an inhibitorof cell death. In embodiments, the compound is an inhibitor of Ire1αinduced cell death. In embodiments, the compound is an inhibitor of apathway induced by Ire1α phosphorylation. In embodiments, the compoundis an inhibitor of a pathway induced by Ire1α kinase activity. Inembodiments, the compound is an inhibitor of a pathway induced by Ire1αRNase activity. In embodiments, the compound is an inhibitor of neuronalcell death. In embodiments, the compound is a cytotoxic agent. Inembodiments, the compound is an anti-cancer agent. In embodiments, thecompound is an inhibitor of demyelination. In embodiments, the compoundis an inhibitor of diabetes. In embodiments, the compound is ananti-diabetic agent. In embodiments, the compound is a neuroprotectiveagent. In embodiments, the compound is an inhibitor of fibrosis. Inembodiments, the compound decreases apoptosis in cells under ER stress.In embodiments, the compound decreases apoptosis in cells under ERstress but not cells under the same conditions except that they are notunder ER stress. In embodiments, the compound decreases apoptosis incells under ER stress more than in cells under the same conditionsexcept that they are not under ER stress. In embodiments, the compounddecreases cleavage of miR-17. In embodiments, the compound decreasesIre1α associated cleavage of miR-17. In embodiments, the compounddecreases cleavage of miR-34a. In embodiments, the compound decreasesIre1α associated cleavage of miR-34a. In embodiments, the compounddecreases cleavage of miR-96. In embodiments, the compound decreasesIre1α associated cleavage of miR-96. In embodiments, the compounddecreases cleavage of miR-125b. In embodiments, the compound decreasesIre1α associated cleavage of miR-125b. In embodiments, the compounddecreases XBP1 mRNA splicing. In embodiments, the compound decreasesIre1α associated XBP1 mRNA splicing. In embodiments, the compounddecreases the UPR. In embodiments, the compound decreases Ire1αassociated UPR. In embodiments, the compound decreases the terminal UPR.In embodiments, the compound decreases Ire1α associated terminal UPR.

In embodiments, the compound is a compound described herein, includingin an aspect, embodiment, example, figure, table, or claim. Inembodiments, the compound is a compound in FIG. 8.

In embodiments, the compounds set forth herein are provided aspharmaceutical compositions including the compound, or apharmaceutically acceptable salt thereof, and a pharmaceuticallyacceptable excipient. In embodiments, the compounds set forth herein arenot provided as pharmaceutical compositions. In embodiments, thecompound is included in a pharmaceutically acceptable salt. Inembodiments, the compound is not included in a pharmaceuticallyacceptable salt.

Described herein, inter alia, is a new strategy to: (1) inhibit IRE1α'shyperactive RNase by pharmacologically targeting its neighboring kinasedomain with small molecules, and (2) test physiological benefits ofshutting down IRE1α in cells (e.g. β-cells) of living mammals (e.g.mice). This work validates IRE1α as a drug target to manipulate ERstress signaling to control cell fate.

In another aspect, provided herein are compounds having the formula (A):

(also illustrated in FIG. 7) and pharmaceutically acceptable saltsthereof, wherein R^(1d), R^(2d), R^(3d), R^(4d), R^(5d), R^(6d), R^(7d),R^(8d), R^(9d), and R^(10d), are each independently C₂₋₆ alkyl, C₁₋₆haloalkyl, —C₁₋₄ alkyl-R^(12d), C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl,aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenylgroups are each optionally substituted with one or two R^(11d) groups;each R^(11d) is independently C₁₋₆ alkyl, C₁₋₆ haloalkyl, —C(O)R^(d),—C(O)OR^(d), —C(O)NR^(d) ₂, S(O)₂NR^(d) ₂, or —S(O)₂R^(d); and R^(12d)is —OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), OC(O)OR^(d), OC(O)NR^(d) ₂,—N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl,monocyclic heteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl,wherein the aryl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groupsare each optionally substituted by one, two, or three groups that areeach independently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; andeach R^(d) is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆haloalkyl, C₃₋₈ cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl,heteroaryl, or heteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl,heteroaryl, and heteroarylalkyl are optionally substituted with one,two, three, or four groups that are each independently halogen, cyano,nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl, —OR^(0d), SR^(0d), NR^(0d)2,C(O)R^(0d), C(O)OR^(0d), —C(O)N(R^(0d))₂, S(O)2R^(0d), —OC(O)R^(0d),—OC(O)OR^(0d), OC(O)N(R^(0d))₂, N(R^(0d))C(O)R^(0d),—N(R^(0d))C(O)OR^(0d), or N(R^(0d))C(O)N(R^(0d))2, wherein each R^(0d)is independently hydrogen or C₁₋₆ alkyl, each R^(d) is independentlyhydrogen, or C₁₋₆ alkyl.

In another aspect, provided herein are compounds having the formula (A):

(also illustrated in FIG. 7) and pharmaceutically acceptable saltsthereof, wherein R^(1d), R^(2d), R^(3d), R^(4d), R^(5d), R^(6d), R^(7d),R^(8d), R^(9d), and R^(10d), are each independently C₂₋₆ alkyl, C₁₋₆haloalkyl, —C₁₋₄ alkyl-R^(12d), C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈cycloalkyl, monocyclic heterocyclyl, monocyclic heteroaryl, or phenyl,aryl, wherein the cycloalkyl, heterocyclyl, heteroaryl, and phenylgroups are each optionally substituted with one or two R^(11d) groups;each R^(11d) is independently C₁₋₆ alkyl, C₁₋₆ haloalkyl, —C(O)R^(d),—C(O)OR^(d), —C(O)NR^(d) ₂, S(O)₂NR^(d) ₂, or —S(O)₂R^(d); and R^(12d)is —OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), OC(O)OR^(d), OC(O)NR^(d) ₂,—N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl,monocyclic heteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl,wherein the aryl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groupsare each optionally substituted by one, two, or three groups that areeach independently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; andeach R^(d) is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆haloalkyl, C₃₋₈ cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl,heteroaryl, or heteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl,heteroaryl, and heteroarylalkyl are optionally substituted with one,two, three, or four groups that are each independently halogen, cyano,nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl, —OR^(0d), SR^(0d), NR^(0d)2,C(O)R^(0d), C(O)OR^(0d), —C(O)N(R^(0d))₂, S(O)2R^(0d), —OC(O)R^(0d),—OC(O)OR^(0d), OC(O)N(R^(0d))₂, N(R^(d))C(O)R^(0d),—N(R^(0d))C(O)OR^(0d), or N(R^(0d))C(O)N(R^(0d))₂, wherein each R^(0d)is independently hydrogen or C₁₋₆ alkyl. In embodiments, each R^(d) isindependently hydrogen or C₁₋₆ alkyl.

In another aspect, R^(2d) and R^(3d) are together a phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)OR^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂, N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; wherein each R^(d)is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆ haloalkyl,C₃₋₈ cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl, heteroaryl, orheteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, andheteroarylalkyl are optionally substituted with one, two, three, or fourgroups that are each independently halogen, cyano, nitro, C₁₋₆ alkyl,C₁₋₆ haloalkyl, —OR^(d), SR, NR^(d) ₂, C(O)R^(0d), C(O)OR^(0d),—C(O)N(R^(0d))₂, S(O)2R^(0d), —OC(O)R^(0d), —OC(O)OR^(0d),OC(O)N(R^(0d))₂, N(R^(0d))C(O)R^(0d), —N(R^(0d))C(O)OR^(0d), orN(R^(0d))C(O)N(R^(0d))₂, wherein each R^(0d) is independently hydrogenor C₁₋₆ alkyl, each R^(d) is independently hydrogen, or C₁₋₆ alkyl.

In another aspect, R^(2d) and R^(3d) are together a phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₆ alkyl, C₁₋₆ haloalkyl, —OR^(d),—SR^(d), —NR^(d) ₂, —C(O) R^(d), C(O)OR^(d), —C(O)NR^(d) ₂, —S(O)₂R^(d),—OC(O) R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂, N(R^(d))C(O) R^(d),—N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; wherein each R^(d) isindependently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆ haloalkyl, C₃₋₈cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl, heteroaryl, orheteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl, heteroaryl, andheteroarylalkyl are optionally substituted with one, two, three, or fourgroups that are each independently halogen, cyano, nitro, C₁₋₆ alkyl,C₁₋₆ haloalkyl, —OR^(0d), SR^(0d), NR^(0d)2, C(O)R^(0d), C(O)OR^(0d),—C(O)N(R^(0d))₂, S(O)2R^(0d), —OC(O)R^(0d), —OC(O)OR^(0d),OC(O)N(R^(0d))₂, N(R^(0d))C(O)R^(0d), —N(R^(0d))C(O)OR^(0d), orN(R^(0d))C(O)N(R^(0d))₂, wherein each R^(0d) is independently hydrogenor C₁₋₆ alkyl. In embodiments, each R^(d) is independently hydrogen orC₁₋₆ alkyl.

In yet another aspect, R^(1d) is —OR^(d), —SR^(d), —NR^(d) ₂,—C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂, —N(R^(d))C(O)R^(d),—N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂.

C. Pharmaceutical Compositions

In another aspect is provided a pharmaceutical composition including apharmaceutically acceptable excipient and a compound, orpharmaceutically acceptable salt thereof, as described herein (e.g.formula I, formula II, formula III, aspect, embodiment, example, figure,table, or claim).

In embodiments of the pharmaceutical compositions, the compound, orpharmaceutically acceptable salt thereof, as described herein (e.g.formula I, formula II, formula III, aspect, embodiment, example, figure,table, or claim) is included in a therapeutically effective amount.

In embodiments of the pharmaceutical compositions, the pharmaceuticalcomposition includes a second agent (e.g. therapeutic agent). Inembodiments of the pharmaceutical compositions, the pharmaceuticalcomposition includes a second agent (e.g. therapeutic agent) in atherapeutically effective amount. In embodiments of the pharmaceuticalcompositions, the second agent is an agent for treating cancer (e.g.multiple myeloma or cancers of secretory cells), neurodegenerativediseases, demyelinating diseases, eye diseases, fibrotic diseases, ordiabetes. In embodiments, the second agent is an anti-cancer agent. Inembodiments, the second agent is a chemotherapeutic. In embodiments, thesecond agent is an agent for improving memory. In embodiments, thesecond agent is an agent for treating a neurodegenerative disease. Inembodiments, the second agent is an agent for treating a demyelinatingdisease. In embodiments, the second agent is an agent for treating aneye disease. In embodiments, the second agent is an agent for treating afibrotic disease. In embodiments, the second agent is an agent fortreating multiple sclerosis. In embodiments, the second agent is anagent for treating Alzheimer's disease. In embodiments, the second agentis an agent for treating Parkinson's disease. In embodiments, the secondagent is an agent for treating Huntington's disease. In embodiments, thesecond agent is an agent for treating a prion disease. In embodiments,the second agent is an agent for treating amyotrophic lateral sclerosis.In embodiments, the second agent is an agent for treating diabetes. Inembodiments, the second agent is an agent for treating retinaldegeneration. In embodiments, the second agent is an agent for treatingretinitis pigmentosa. In embodiments, the second agent is an agent fortreating macular degeneration. In embodiments, the second agent is anagent for treating type I diabetes. In embodiments, the second agent isan agent for treating type II diabetes. In embodiments, the second agentis an agent for treating multiple myeloma. In embodiments, the secondagent is an agent for treating a cancer of a secretory cell. Inembodiments, the second agent is an agent for reducing Ire1 (e.g. Ire1α)kinase activity. In embodiments, the second agent is an agent forreducing Ire1 (e.g. Ire1α) RNase activity. In embodiments, the secondagent is an agent for inhibiting a pathway activated by Ire1 (e.g.Ire1α) phosphorylation. In embodiments, the second agent is an agent forinhibiting a pathway activated by Ire1 (e.g. Ire1α) RNase activity. Inembodiments, the second agent is an agent for inhibiting Ire1 (e.g.Ire1α) oligomerization. In embodiments, the second agent is an agent forinhibiting apoptosis.

D. Methods

In an aspect is provided a method of treating a disease in a patient inneed of such treatment, the method including administering atherapeutically effective amount of a compound described herein (e.g.formula I, formula II, formula III, aspect, embodiment, example, figure,table, or claim), or a pharmaceutically acceptable salt thereof, to thepatient, wherein the disease is a neurodegenerative disease,demyelinating disease, cancer, eye disease, fibrotic disease, ordiabetes.

In embodiments, the disease is a neurodegenerative disease,demyelinating disease, cancer, or diabetes. In embodiments, the diseaseis a neurodegenerative disease. In embodiments, the neurodegenerativedisease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinaldegeneration, macular degeneration, Parkinson's Disease, AlzheimerDisease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease,or Kuru. In embodiments, the disease is amyotrophic lateral sclerosis.In embodiments, the disease is retinal degeneration. In embodiments, thedisease is retinitis pigmentosa. In embodiments, the disease is ademyelinating disease. In embodiments, the demyelinating disease isWolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis,Charcot-Marie-Tooth Disease, or Multiple Sclerosis. In embodiments, thedisease is Multiple Sclerosis. In embodiments, the disease is cancer. Inembodiments, the cancer is multiple myeloma. In embodiments, the diseaseis diabetes. In embodiments, the diabetes is type I diabetes. Inembodiments, the diabetes is type II diabetes. In embodiments, thedisease is a neurodegenerative disease, demyelinating disease, cancer,eye disease, fibrotic disease, or diabetes described herein. Inembodiments, the disease is an eye disease. In embodiments, the eyedisease is retinitis pigmentosa. In embodiments, the eye disease isretinal degeneration. In embodiments, the eye disease is maculardegeneration. In embodiments, the eye disease is Wolfram Syndrome. Inembodiments, the disease is idiopathic pulmonary fibrosis (IPF). Inembodiments, the disease is a fibrotic disease. In embodiments, thefibrotic disease is idiopathic pulmonary fibrosis (IPF), myocardialinfarction, cardiac hypertrophy, heart failure, cirrhosis, acetominophen(Tylenol) liver toxicity, hepatitis C liver disease, hepatosteatosis(fatty liver disease), or hepatic fibrosis. In embodiments, the diseaseis interstitial lung disease (ILD). In embodiments, the disease ismyocardial infarction. In embodiments, the disease is cardiachypertrophy. In embodiments, the disease is heart failure. Inembodiments, the disease is cirrhosis. In embodiments, the disease isacetominophen (Tylenol) liver toxicity. In embodiments, the disease ishepatitis C liver disease. In embodiments, the disease ishepatosteatosis (fatty liver disease). In embodiments, the disease ishepatic fibrosis.

In an aspect is provided a method of modulating the activity of an Ire1(e.g. Ire1α) protein, the method including contacting the Ire1 (e.g.Ire1α) protein with an effective amount of a compound described herein(e.g. formula I, formula II, formula III, aspect, embodiment, example,figure, table, or claim), or a pharmaceutically acceptable salt thereof.

In embodiments, the modulating is inhibiting. In embodiments, theactivity is kinase activity. In embodiments, the kinase activity isautophosphorylation activity. In embodiments, the kinase activity istrans-autophosphorylation activity. In embodiments, the activity isoligomerization activity. In embodiments, the oligomerization activityis dimerization activity. In embodiments, the activity is RNaseactivity. In embodiments, the activity is miR-17 cleavage. Inembodiments, the activity is miR-34a cleavage. In embodiments, theactivity is miR-96 cleavage. In embodiments, the activity is miR-125bcleavage. In embodiments, the activity is XBP1 mRNA splicing. Inembodiments, the activity is UPR activation. In embodiments, theactivity is terminal UPR activation. In embodiments, a cell includes theIre1 (e.g. Ire1α) protein. In embodiments, the activity of the Ire1(e.g. Ire1α) protein is increasing apoptosis of the cell. Inembodiments, an organ includes the cell. In embodiments, an organismincludes the cell. In embodiments, an organism has a disease associatedwith the Ire1 (e.g. Ire1α) protein activity. In embodiments, the diseaseis a neurodegenerative disease, a demyelinating disease, cancer, an eyedisease, a fibrotic disease, or diabetes. In embodiments, the disease isa neurodegenerative disease. In embodiments, the neurodegenerativedisease is retinitis pigmentosa, amyotrophic lateral sclerosis, retinaldegeneration, macular degeneration, Parkinson's Disease, AlzheimerDisease, Huntington's Disease, Prion Disease, Creutzfeldt-Jakob Disease,or Kuru. In embodiments, the disease is amyotrophic lateral sclerosis.In embodiments, the disease is retinal degeneration. In embodiments, thedisease is retinitis pigmentosa. In embodiments, the disease is ademyelinating disease. In embodiments, the demyelinating disease isWolfram Syndrome, Pelizaeus-Merzbacher Disease, Transverse Myelitis,Charcot-Marie-Tooth Disease, or Multiple Sclerosis. In embodiments, thedisease is Multiple Sclerosis. In embodiments, the disease is cancer. Inembodiments, the cancer is multiple myeloma. In embodiments, the diseaseis diabetes. In embodiments, the diabetes is type I diabetes. Inembodiments, the diabetes is type II diabetes. In embodiments, thedisease is an eye disease. In embodiments, the eye disease is retinitispigmentosa. In embodiments, the eye disease is retinal degeneration. Inembodiments, the eye disease is macular degeneration. In embodiments,the eye disease is Wolfram Syndrome. In embodiments, the disease isidiopathic pulmonary fibrosis (IPF). In embodiments, the disease is afibrotic disease. In embodiments, the fibrotic disease is idiopathicpulmonary fibrosis (IPF), myocardial infarction, cardiac hypertrophy,heart failure, cirrhosis, acetominophen (Tylenol) liver toxicity,hepatitis C liver disease, hepatosteatosis (fatty liver disease), orhepatic fibrosis. In embodiments, the disease is interstitial lungdisease (ILD). In embodiments, the disease is myocardial infarction. Inembodiments, the disease is cardiac hypertrophy. In embodiments, thedisease is heart failure. In embodiments, the disease is cirrhosis. Inembodiments, the disease is acetominophen (Tylenol) liver toxicity. Inembodiments, the disease is hepatitis C liver disease. In embodiments,the disease is hepatosteatosis (fatty liver disease). In embodiments,the disease is hepatic fibrosis. In embodiments, the Ire1 protein is anIre1α protein. In embodiments, the Ire1 (e.g. Ire1α) protein is a humanprotein. In embodiments, the Ire1 protein is a human Ire1α protein.

In another aspect, the present disclosure, has identified two classes ofkinase inhibitors—called types I and II, which stabilize alternatekinase active site conformations in numerous protein kinase targets(Liu, Y. & Gray, N. S. Nat. Chem. Biol. 2, 358-364 (2006)). The presentdisclosure shows that a type I kinase inhibitor and a novel type IIkinase inhibitor both modify IRE1α by shutting down IRE1αtrans-autophosphorylation, but have divergent effects on its RNase toactivate or inactivate catalytic activity, respectively. The presentdisclosure further demonstrates that IRE1α RNase activity can be eitherup or downregulated through selective targeting of its kinase domain tocontrol UPR signaling, and predict that it may be possible topharmacologically modulate other kinase-coupled enzymes in a similarway.

In an additional aspect, the present disclosure illustrates that IRE1α'skinase-controlled RNase can be regulated in two distinct modes withkinase inhibitors: one class of ligands occupy IRE1α's kinaseATP-binding site to activate RNase-mediated XBP1 mRNA splicing evenwithout upstream ER stress, while a second class can inhibit the RNasethrough the same ATP-binding site, even under ER stress. Thus,alternative kinase conformations stabilized by distinct classes ofATP-competitive inhibitors can cause allosteric switching of IRE1α'sRNase—either on or off. As dysregulation of the UPR has been implicatedin a variety of cell degenerative and neoplastic disorders, smallmolecule control over IRE1α should advance efforts to understand theUPR's role in pathophysiology and to develop drugs for ER stress-relateddiseases.

E. Additional Embodiments

1. A compound having the formula:

wherein, ring A is substituted or unsubstituted cycloalkylene,substituted or unsubstituted heterocycloalkylene, substituted orunsubstituted arylene, or substituted or unsubstituted heteroarylene; L¹is a bond or unsubstituted C₁-C₅ alkylene; L² is a bond, —NR^(6a)—, —O—,—S—, —C(O)—, —S(O)—, —S(O)₂—, —NR^(6a)C(O)—, —C(O)NR^(6b)—,—C(O)(CH₂)_(z2)—, —NR^(6a)C(O)O—, —NR^(6a)C(O)NR^(6b)—, substituted orunsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene; R¹ is hydrogen, oxo,halogen, —CX₃, —CN, —S₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO_(n)R¹⁰, —NR⁷C═(O)R⁹, —NR⁷C(O)OR⁹, —NR⁷OR⁹,—OCX₃, —OCHX₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R² ishydrogen, oxo, halogen, —CX^(a) ₃, —CN, —SO₂Cl, —SO_(n1)R^(10a),SO_(v1)NR^(7a)R^(8a), —NNH₂, —ONR^(7a)R^(8a), —NHC═(O)NHNH₂,—NHC═(O)NR^(7a)R^(8a), —N(O)_(m1), —NR^(7a)R^(8a)—C(O)R^(9a),—C(O)OR^(9a), —C(O)NR^(7a)R^(8a), —OR^(10a), —NR^(7a)SO_(n1)R^(10a),—NR^(7a)C═(O)R^(9a), —NR^(7a)C(O)OR^(9a), —NR^(7a)OR^(9a), —OCX^(a) ₃,—OCHX^(a) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R³ isindependently hydrogen, oxo,halogen, —CX^(b) ₃, —CN, —SO₂Cl, —SO_(n2)R^(10b), —SO_(v2)NR^(7b)R^(8b),—NHNH₂, —ONR^(7b)R^(8b), —NHC═(O)NHNH₂,—NHC═(O)NR^(7b)R^(8b), —N(O)_(m2), —NR^(7b)R^(8b), —C(O)R^(9b),—C(O)—OR^(9b), —C(O)NR^(7b)R^(8b), —OR^(10b), —NR^(7b)SO_(n2)R^(10b),—NR^(7b)C═(O)R^(9b), —NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —OCX^(b) ₃,—OCHX^(b) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁴ andR⁵ are independently hydrogen or unsubstituted C₁-C₆ alkyl; R⁷, R⁸, R⁹,R¹⁰, R^(6a), R^(7a), R^(8a), R^(9a), R^(10a), R^(6b), R^(7b), R^(8b),R^(9b) and R^(10b) are independently hydrogen, halogen, —CF₃, —CN, —OH,—NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R⁷ andR⁸ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7b) and R^(8b) substituents bonded to thesame nitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; each occurrence of the symbols n, n1, and n2 isindependently an integer from 0 to 4; each occurrence of the symbols m,m1, m2, v, v1, and v2 is independently an integer from 1 to 2; thesymbol z is an integer from 0 to 2; the symbol z2 is an integer from 1to 4; and each occurrence of the symbols X, X^(a), and X^(b) isindependently a halogen.

2. The compound of embodiment 1, wherein R³ is independently hydrogen,halogen, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl.

3. The compound of any one of embodiments 1 to 2, wherein R³ ishydrogen.

4. The compound of any one of embodiments 1 to 3, wherein the symbol zis 1.

5. The compound of any one of embodiments 1 to 4, wherein R² ishydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl.

6. The compound of any one of embodiments 1 to 5, wherein R² issubstituted or unsubstituted alkyl.

7. The compound of any one of embodiments 1 to 6, wherein R² issubstituted or unsubstituted C₁-C₆ alkyl.

8. The compound of any one of embodiments 1 to 7, wherein R² isunsubstituted C₁-C₆ alkyl.

9. The compound of any one of embodiments 1 to 8, wherein R² isunsubstituted isopropyl or unsubstituted tert-butyl.

10. The compound of anyone of embodiments 1 to 9, wherein R⁴ and R⁵ arehydrogen.

11. The compound of anyone of embodiments 1 to 10, wherein L¹ is a bond.

12. The compound of any one of embodiments 1 to 10, wherein L¹ isunsubstituted methylene.

13. The compound of any one of embodiments 1 to 12, wherein L² is—NR^(6a)C(O)NR⁶—.

14. The compound of any one of embodiments 1 to 13, wherein R^(6a) andR^(6b) are hydrogen.

15. The compound of any one of embodiments 1 to 14, wherein R¹ issubstituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl.

16. The compound of any one of embodiments 1 to 15, wherein R¹ issubstituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl.

17. The compound of any one of embodiments 1 to 16, wherein R¹ issubstituted or unsubstituted aryl or substituted or unsubstitutedheteroaryl.

18. The compound of any one of embodiments 1 to 17, wherein R¹ issubstituted phenyl.

19. The compound of any one of embodiments 1 to 18, wherein R¹ is phenylsubstituted with —CF₃ or halogen.

20. The compound of any one of embodiments 1 to 19, wherein ring A issubstituted or unsubstituted arylene or substituted or unsubstitutedheteroarylene.

21. The compound of anyone of embodiments 1 to 20, wherein ring A issubstituted or unsubstituted C₆-C₁₀ arylene.

22. The compound of anyone of embodiments 1 to 21, wherein ring A isunsubstituted naphthalenyl.

23. The compound of anyone of embodiments 1 to 22 having the formula:

wherein, L³ is a bond, —NR^(6b)—, substituted or unsubstituted alkylene,substituted or unsubstituted heteroalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, orsubstituted or unsubstituted heteroarylene.

24. The compound of any one of embodiments 1 to 23 having the formula:

25. The compound of any one of embodiments 1 to 24 selected from thegroup consisting of:

26. A pharmaceutical composition comprising a pharmaceuticallyacceptable excipient and a compound of any one of embodiments 1 to 25.

27. A method of treating a disease in a patient in need of suchtreatment, said method comprising administering a therapeuticallyeffective amount of a compound of any one of embodiments 1 to 25 to saidpatient, wherein the disease is a neurodegenerative disease,demyelinating disease, cancer, eye disease, fibrotic disease, ordiabetes.

28. The method of embodiment 27, wherein the disease is aneurodegenerative disease.

29. The method of any one of embodiments 27 and 28, wherein theneurodegenerative disease is retinitis pigmentosa, amyotrophic lateralsclerosis, retinal degeneration, macular degeneration, Parkinson'sDisease, Alzheimer Disease, Huntington's Disease, Prion Disease,Creutzfeldt-Jakob Disease, or Kuru.

30. The method of embodiment 27, wherein the disease is a demyelinatingdisease.

31. The method of anyone of embodiments 27 and 30, wherein thedemyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease,Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis.

32. The method of embodiment 27, wherein the disease is cancer.

33. The method of any one of embodiments 27 and 32, wherein the canceris multiple myeloma.

34. The method of embodiment 27, wherein the disease is diabetes.

35. The method of anyone of embodiments 27 and 34, wherein the diabetesis type I diabetes.

36. The method of any one of embodiments 27 and 34, wherein the diabetesis type II diabetes.

37. The method of embodiment 27, wherein the disease is an eye disease.

38. The method of anyone of embodiments 27 and 37, wherein the eyedisease is retinitis pigmentosa, retinal degeneration, maculardegeneration, or Wolfram Syndrome.

39. The method of embodiment 27, wherein the disease is a fibroticdisease.

40. The method of any one of embodiments 27 and 39, wherein the fibroticdisease is idiopathic pulmonary fibrosis (IPF), myocardial infarction,cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol)liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liverdisease), or hepatic fibrosis.

41. A method of modulating the activity of an Ire1 protein, said methodcomprising contacting said Ire1 protein with an effective amount of acompound of any one of embodiments 1 to 25.

42. The method of embodiment 41, wherein said modulating is inhibiting.

43. The method of anyone of embodiments 41 to 42, wherein said activityis kinase activity.

44. The method of embodiment 43, wherein said kinase activity isautophosphorylation activity.

45. The method of anyone of embodiments 41 to 42, wherein said activityis oligomerization activity.

46. The method of embodiment 45, wherein said oligomerization activityis dimerization activity.

47. The method of any one of embodiments 41 to 42, wherein said activityis RNase activity.

48. The method of any one of embodiments 41 to 42, wherein a cellcomprises said Ire1 protein.

49. The method of embodiment 48, wherein said activity of the Ire1protein is increasing apoptosis of said cell.

50. The method of any one of embodiments 48 to 49, wherein an organcomprises said cell.

51. The method of anyone of embodiments 48 to 50, wherein an organismcomprises said cell.

52. The method of embodiment 51, wherein said organism has a diseaseassociated with said Ire1 protein activity.

53. The method of embodiment 52, wherein said disease is aneurodegenerative disease, demyelinating disease, cancer, eye disease,fibrotic disease, or diabetes.

54. The method of embodiment 53, wherein the disease is aneurodegenerative disease.

55. The method of any one of embodiments 53 and 54, wherein theneurodegenerative disease is retinitis pigmentosa, amyotrophic lateralsclerosis, retinal degeneration, macular degeneration, Parkinson'sDisease, Alzheimer Disease, Huntington's Disease, Prion Disease,Creutzfeldt-Jakob Disease, or Kuru.

56. The method of embodiment 53, wherein the disease is cancer.

57. The method of any one of embodiments 53 and 56, wherein the canceris multiple myeloma.

58. The method of embodiment 53, wherein the disease is diabetes.

59. The method of any one of embodiments 53 and 58, wherein the diabetesis type I diabetes.

60. The method of any one of embodiments 53 and 58, wherein the diabetesis type II diabetes.

61. The method of embodiment 53, wherein the disease is a demyelinatingdisease.

62. The method of anyone of embodiments 53 and 61, wherein thedemyelinating disease is Wolfram Syndrome, Pelizaeus-Merzbacher Disease,Transverse Myelitis, Charcot-Marie-Tooth Disease, or Multiple Sclerosis.

63. The method of any one of embodiments 53, 61, and 62, wherein thedemyelinating disease is Multiple Sclerosis.

64. The method of embodiment 53, wherein the disease is an eye disease.

65. The method of any one of embodiments 53 and 64, wherein the eyedisease is retinitis pigmentosa, retinal degeneration, maculardegeneration, or Wolfram Syndrome.

66. The method of embodiment 53, wherein the disease is a fibroticdisease.

67. The method of any one of embodiments 53 and 66, wherein the fibroticdisease is idiopathic pulmonary fibrosis (IPF), myocardial infarction,cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol)liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liverdisease), or hepatic fibrosis.

68. A compound of the formula

or a pharmaceutically acceptable salt thereof, wherein R^(1d), R^(2d),R^(3d), R^(4d), R^(5d), R^(6d), R^(7d), R^(8d), R^(9d), and R^(10d), areeach independently C₂₋₆ alkyl, C₁₋₆ haloalkyl, —C₁₋₄ alkyl-R^(12d), C₂₋₆alkenyl, C₂₋₆ alkynyl, C₃₋₈ cycloalkyl, monocyclic heterocyclyl,monocyclic heteroaryl, or phenyl, aryl, wherein the cycloalkyl,heterocyclyl, heteroaryl, and phenyl groups are each optionallysubstituted with one or two R^(11d) groups; each R^(11d) isindependently C₁₋₆ alkyl, C₁₋₆ haloalkyl, —C(O)R^(d), —C(O)OR^(d),—C(O)NR^(d) ₂, S(O)₂NR^(d) ₂, or —S(O)₂R^(d); and R^(12d) is —OR^(d),—SR^(d), —NR^(d) ₂, —C(O)R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂, —S(O)₂R^(d),—OC(O)R^(d), OC(O)OR^(d), OC(O)NR^(d) ₂, —N(R^(d))C(O)R^(d),—N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl, monocyclicheteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl, wherein thearyl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groups are eachoptionally substituted by one, two, or three groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O) R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂,N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; andeach R^(d) is independently hydrogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆haloalkyl, C₃—. cycloalkyl, heterocyclyl, aryl, arylC₁₋₆ alkyl,heteroaryl, or heteroarylC₁₋₆ alkyl wherein the alkyl, aryl, arylalkyl,heteroaryl, and heteroarylalkyl are optionally substituted with one,two, three, or four groups that are each independently halogen, cyano,nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl, —OR^(0d), SR^(0d), NR^(0d)2,C(O)R^(0d), C(O)OR^(0d), —C(O)N(R^(0d))2, S(O)2R^(0d), —OC(O)R^(0d),—OC(O)OR^(0d), OC(O)N(R^(0d))2, N(R^(0d))C(O)R^(0d),—N(R^(0d))C(O)OR^(0d), or N(R^(0d))C(O)N(R^(0d))2, wherein each R^(0d)is independently hydrogen or C₁₋₆ alkyl, each R^(d) is independentlyhydrogen, or C₁₋₆ alkyl.

69. A compound of the formula

or a pharmaceutically acceptable salt thereof, wherein R^(1d) is—OR^(d), —SR^(d), —NR^(d) ₂, —C(O) R^(d), —C(O)OR^(d), —C(O)NR^(d) ₂,—N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), —N(R^(d))C(O)NR^(d) ₂, phenyl,monocyclic heteroaryl, C₃₋₈ cycloalkyl, or monocyclic heterocyclyl,wherein the aryl, heteroaryl, C₃₋₈ cycloalkyl, and heterocyclyl groupsare each optionally substituted by one, two, or three groups that areeach independently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(d), —SR^(d), —NR^(d) ₂, —C(O)R^(d), C(O)OR^(d), —C(O)NR^(d) ₂,—S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d), OC(O)NR^(d) ₂, N(R^(d))C(O)R^(d), —N(R^(d))C(O)OR^(d), or —N(R^(d))C(O)NR^(d) ₂; and R^(2d) andR^(3d) are together a phenyl, monocyclic heteroaryl, C₃₋₈ cycloalkyl, ormonocyclic heterocyclyl, wherein the aryl, heteroaryl, C₃₋₈ cycloalkyl,and heterocyclyl groups are each optionally substituted by one, two, orthree groups that are each independently halogen, cyano, nitro, C₁₋₆alkyl, C₁₋₆ haloalkyl, —OR^(d), —SR^(d), —NR^(d) ₂—C(O)R^(d),C(O)OR^(d), —C(O)NR^(d) ₂, —S(O)₂R^(d), —OC(O)R^(d), —OC(O)OR^(d),OC(O)NR^(d) ₂, N(R^(d))C(O) R^(d), —N(R^(d))C(O)OR^(d), or—N(R^(d))C(O)NR^(d) ₂; wherein each R^(d) is independently hydrogen,C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆ haloalkyl, C₃₋₈ cycloalkyl, heterocyclyl,aryl, arylC₁₋₆ alkyl, heteroaryl, or heteroarylC₁₋₆ alkyl wherein thealkyl, aryl, arylalkyl, heteroaryl, and heteroarylalkyl are optionallysubstituted with one, two, three, or four groups that are eachindependently halogen, cyano, nitro, C₁₋₆ alkyl, C₁₋₆ haloalkyl,—OR^(0d), SR^(0d), NR^(0d)2, C(O)R^(0d), C(O)OR^(0d), —C(O)N(R^(0d))2,S(O)2R^(0d), —OC(O)R^(0d), —OC(O)OR^(0d), OC(O)N(R^(0d))2,N(R^(0d))C(O)R^(0d), —N(R^(0d))C(O)OR^(0d), or N(R^(0d))C(O)N(R^(0d))2,wherein each R^(0d) is independently hydrogen or C₁₋₆ alkyl, each R^(d)is independently hydrogen, or C₁₋₆ alkyl.

70. A composition comprising any of the formulas of embodiments 68 and69 or a pharmaceutically acceptable salt thereof.

71. A pharmaceutical composition for inhibiting IRE1α RNase activity,the composition comprising: Formula (A), Formula (B), any derivatives ofFormula (A) and Formula (B) disclosed herein, GP17, GP21, GP29, DSA7,DSA8, GP117, GP118, GP146, GP146 (NMe), GP146(Am), compounds shown FIGS.7 and 8, any of the formulas from embodiments 68 and 69, andcombinations thereof.

72. A pharmaceutical composition for activating IRE1α RNase activity,the composition comprising murine IRE1α.

73. A method for inhibiting IRE1α RNase activity, the method comprisingproviding a subject in need of such inhibition an effective amount ofeither: a. a compound of embodiment 68, Formula (A), Formula (B), GP17,GP21, GP29, DSA7, DSA8, GP117, GP118, GP146, GP146 (NMe), GP146(Am), acompound shown FIG. 7 or 8, any of the formulas of embodiments 68 and69, and any combinations thereof, or b. a pharmaceutical compositioncomprising a compound from 73(a) and a pharmaceutically acceptableexcipient, carrier, or diluent.

74. A method for activating IRE1α RNase activity, the method comprisingproviding a subject in need of such inhibition an effective amount ofeither: a. murine IRE1α; or b. a pharmaceutical compostion comprisingmurine IRE1α and a pharmaceutically acceptable excipient, carrier, ordiluent.

75. The method of any one of embodiments 41 to 67, wherein said Ire1 isIre1α.

76. The method of any one of embodiments 41 to 67 and 75, wherein saidIre1 is a human Ire1.

F. Examples

1. Screening and Optimization of IRE1α Modulators

The particulars shown herein are by way of example and for purposes ofillustrative discussion of embodiments of the present invention only andare presented in the cause of providing what is believed to be a readilyunderstood description of the principles and conceptual aspects ofvarious embodiments of the invention. In this regard, no attempt is madeto show structural details of the invention in more detail than isnecessary for the fundamental understanding of the invention, thedescription taken with the drawings and/or examples making apparent tothose skilled in the art how the several forms of the invention may beembodied in practice.

Inhibition of IRE1α's RNase activity through the ATP-binding site of itskinase domain using kinase inhibitors. Generation of more potent andselective analogs of IRE1α kinase inhibitors Discovery ofATP-competitive kinase inhibitors that are able to inhibit the RNasedomain of IRE1α from a distance. Previous studies have demonstrated thatthe RNase activity of IRE1α is dependent on kinase domainautophosphorylation. Shown herein is an unexpected relationship betweenthe kinase and RNase domains, where ligands that interact with theATP-binding site of the kinase domain are able to bypass theautophosphorylation requirement and activate the RNase domain (Papa, F.R. et al. Science 302, 1533-1537 (2003)). For instance, the orthogonalATP-competitive inhibitor 1NM-PP1 is able to rescue the RNase activityof IRE1α mutants that lack kinase activity (Han, D. et al. Biochemicaland biophysical research communications 365, 777-783, (2008)). Otherligands that interact with the ATP-binding site of wild-type IRE1α,including the endogenous co-factors ADP and ATP, are also able toactivate RNase activity directly (Lee, K. P. et al. Cell 132, 89-100,(2008); Ali, M. M. et al. The EMBO journal 30, 894-905, (2011)). Also,the ATP-competitive inhibitors APY29 and sunitinib directly activate theRNase of yeast and murine IRE1α (Han, D. et al. Cell 138, 562-575,(2009); Korennykh, A. V. et al. Nature 457, 687-693, (2009)). A crystalstructure of APY29 bound to yeast IRE1 shows that the kinase catalyticdomain is in an active conformation (Korennykh, A. V. et al. Nature 457,687-693, (2009)), which is a conformation adopted by protein kinasescapable of catalyzing phosphate transfer. By stabilizing an activeconformation of IRE1α's ATP-binding site, certain co-factors andATP-competitive inhibitors act as ligands that allosterically activateits adjacent RNase domain. Given the ability to allosterically activateIRE1α's RNase through its kinase domain, it should be possible to alsoinhibit the RNase through the same kinase domain with a different classof kinase inhibitors that stabilize an inactive ATP-binding siteconformation. Two classes of ATP-competitive kinase inhibitors—calledtypes I and II—have been identified (FIG. 1A), which stabilize alternatekinase active site conformations in numerous protein kinasetargets^(51,52). Type I inhibitors-like APY29 and sunitinib-stabilize anactive ATP-binding site conformation. In contrast, type IIinhibitors-like the clinically-approved drugs imatinib andsorafenib-selectively stabilize an inactive ATP-binding siteconformation⁵³⁻⁵⁵. The inactive ATP-binding site conformation stabilizedby type II inhibitors is characterized by outward movement of thecatalytically-important Asp-Phe-Gly (DFG) motif, and is therefore calledthe DFG-out conformation (FIG. 1A)^(51,52). Described herein is thegeneration of a diverse panel of type II inhibitors and characterizationof their interactions with a number of protein kinases (Krishnamurty, R.et al. Nature chemical biology 9, 43-50, (2013); Han, D. et al.Biochemical and biophysical research communications 365, 777-783,(2008); Brigham, J. L. et al. ACS Chem. Biol. (2013); Hill, Z. B. et al.ACS Chem. Biol. 7, 487-495 (2012)). These pharmacological tools servedas a starting point towards the goal of identifying ATP-competitiveinhibitors able to allosterically inactivate the IRE1α RNase.

The diverse panel of type II inhibitors were screened for their abilityto block the RNase activity of a recombinant soluble human IRE1αmini-protein construct (expressed in baculovirus) containing thekinase/RNase domains—called IRE1α* (Zhang, J. et al. Nature reviews.Cancer 9, 28-39, (2009)). Since IRE1α* is basally autophosphorylated,its RNase is active, and can be assayed using a FRET-quenched XBP1 RNAmini-substrate. While all the type II inhibitors tested with this assaycontain the core binding elements predicted to stabilize the DFG-outconformation, only one ligand, demonstrated measurable inhibition ofIRE1α*'s RNase activity at a concentration of 60 μM (FIGS. 1C and 1D).Because these type II kinase inhibitors also attenuate the RNaseactivity of IRE1α*, they were designated KIRAs—for kinase-inhibitingRNase attenuators. KIRA1 is a pyrazolopyrimidine-based inhibitor thathas been shown to stabilize the DFG-out conformation of the non-receptortyrosine kinases Src and Abl (Dar, A. C. et al. Chemistry & Biology 15,1015-1022 (2008)). Based on the co-crystal structure of KIRA1 bound toSrc (PDB: 3EL8) and molecular modeling, proposed contacts with IRE1α areshown in FIG. 1A.

Despite its modest potency, KIRA1 served as a suitable starting pointfor developing higher affinity allosteric RNase inhibitors. A number ofsimilar analogs were generated and tested for RNase inhibition. Whilemost modifications of KIRA1 were deleterious, replacing thepyrazolopyrimidine scaffold with an imidazopyrazine core provided asignificant increase in overall potency (KIRA2, FIGS. 1C and 1D).Furthermore, substituting the 4-anilino group at the C-3 position ofKIRA2 with a naphthylamine moiety provided KIRA3. Notably, KIRA3inhibits XBP1 RNA cleavage to a similar degree as STF-083010, animine-based small molecule that directly inhibits the IRE1α RNasethrough covalent modification.

Similar to the type I inhibitor APY29 (IC₅₀ (autophosphorylation)=0.28μM), KIRA3 (IC₅₀ (autophosphorylation)=3.1 μM) demonstratesdose-dependent reduction of IRE1α* kinase autophosphorylation in vitro.Thus, although KIRA3 and APY29 are both IRE1α* kinase inhibitors, theydemonstrate opposing effects on its RNase activity, with APY29 acting asan activator. To further characterize differences between the two kinaseinhibitors, a version of IRE1α* was generated with low basal RNaseactivity by using λ-phosphatase to remove activating phosphates. Asexpected, the dephosphorylated variant of IREα* (dP-IRE1α*) hassignificantly lower basal RNase activity than IRE1α*; incubatingdP-IRE1α* with increasing APY29 progressively restores its ability tocleave the XBP1 mini-substrate, plateauing at 60% of the levels of IRE1*(FIG. 2C). In contrast, KIRA3 suppresses residual RNase activity ofdP-IRE1α*.Competition experiments were performed to further explore theopposing effects of APY29 and KIRA3. Increasing concentrations of APY29progressively reverse IRE1α* RNase inhibition caused by a fixedconcentration of KIRA3 (FIG. 2E). Furthermore, the type I inhibitorsunitinib also opposes the RNase inhibitory effect of KIRA3. On theother hand, increasing concentrations of KIRA3 restore RNase inhibitionunder a fixed concentration of APY29, with an expected increase in theIC₅₀. As predicted, APY29 cannot rescue direct inhibition caused by thecovalent RNase modifier STF-083010. Taken together, these resultsstrongly suggest that APY29 and KIRA3 are exerting their opposingeffects on RNase activity through the same binding site.

The drug sunitinib is a promiscuous type I inhibitor that has been shownto inhibit the kinase activity of yeast and human IRE116,19. Toinvestigate the differences between GP146 (KIRA3) and otherATP-competitive inhibitors of IRE1α, the interaction of sunitinib withthe IRE1α* and dP-IRE1α* constructs was further characterized. Asexpected, sunitinib is a dose-dependent inhibitor of theautophosphorylation activity of IRE* (FIG. 18a ). In addition, sunitinibactivates the RNase activity of dP-IRE1α*, which is consistent with itstype I pharmacophore (FIG. 18b ). Therefore, both APY29 and sunitinibstabilize an ATP-binding site conformation that activates the RNasedomain of IRE1α. Like APY29, increasing amounts of sunitinib are able torescue the RNase activity of IRE1α* in the presence of a fixedconcentration of GP146 (FIG. 18c ). Together, these results show thatGP146 opposes the stereotypic RNase activation demonstrated by varioustype I ATP-competitive inhibitors of IRE1α.

KIRA3 prevents dimerization and oligomerization of IRE1α.Self-association of kinase/RNase monomers has been reported to increaseRNase activity as dimers and/or higher-order oligomers form in yeast andmammalian IRE1 proteins. furthermore, the degree of order may correlatedirectly with activity. Thus, APY29 and KIRA3 were used to test theprediction that they would divergently affect the oligomerization stateof human IRE1α as a basis for their opposing effects on its RNaseactivity. Specifically, RNase activators should drive monomers intohigher-order species from baseline. To test this, increasingconcentrations of IRE1α* were incubated with either DMSO, or saturatingconcentrations of APY29 or KIRA3 and the ratio of oligomeric—defined asall species greater than monomers—to monomeric IRE1α was determined(FIG. 24). In the absence of ligands, IRE1* shows aconcentration-dependent increase in the oligomer/monomer ratio. APY29further enhances—whereas KIRA3 decreases—this concentration-dependentincrease in the IRE1α* oligomer/monomer ratio. Taken together, the invitro data support a model in which these two classes of kinaseinhibitors divergently modulate IRE1α* RNase activity by exertingopposing effects on the oligomerization state of the enzyme.

2. Synthesis and Characterization of Compositions

Unless otherwise noted, all reagents were obtained from commercialsuppliers and used without purification. TLC was performed on EMDMillipore silica gel 60 F254 plates. 1H-NMR spectra were obtained on aBruker AV-300 or AV301 instrument at room temperature and 13C-NMRspectra were obtained on a Bruker AV-500 instrument at room temperature.Chemical shifts are reported in ppm, and coupling constants are reportedin Hz. 1H and 13C resonances are referenced to residual MeOH. Massspectrometry was performed on a Bruker Esquire Ion Trap MS instrument.The purity of all final compounds was determined by analytical IPLC withtwo different solvent systems. Analytical conditions A: [C18 (150×2.1mm), CH3CN/H2O—0.1% CF3CO2H=1:99 to 100:0 over 33 min; 1 mL/min; 220 and254 nm detection for 33 min]. Analytical conditions B: [C18 (150×2.1mm), CH3OH/H2O—0.1% CF3CO2H=1:99 to 100:0 over 33 min; 1 mL/min; 220 and254 nm detection for 33 min].

STF-083010, Sunitinib, nilotinib, and GP21 were obtained from commercialsuppliers. All compounds were verified to be >95% pure by analyticalHPLC. APY29 and GP118 was prepared according to a previously reportedprocedures.

1-iodo-3-isopropylimidazo[1,5-a]pyrazin-8-amine (compound 1). Compound 1was synthesized according to a previously described procedure.1-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)urea(compound 2). A mixture of 4-Aminophenylboronic acid pinacol ester (50.0mg, 0.23 mmol) and 3-(Trifluoromethyl)phenyl isocyanate (46.0 uL, 0.31mmol) in THF (1.9 mL) was stirred overnight at room temperature. Themixture was concentrated, diluted with dichloromethane and washed withwater. The organic layer was dried over Na2SO4, concentrated in vacuoand the resultant crude product was purified by flash chromatography(20% ethyl acetate in hexanes) to afford 92.5 mg of compound 2 (98%yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf=0.4; 1H NMR (300 MHz, MeOD):δ 7.90 (s, 1H), 7.71-7.68 (m, 2H), 7.60 (d, J=6.0 Hz, 1H), 7.48-7.42 (m,3H), 7.29 (d, J=9.0 Hz, 1H), 1.34 (s, 12H); ESI-MS (m/z): [M]+ calcd.for C20H22BF3N2O3, 406.17; [M+1]+ found, 407.5.1-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)naphthalen-1-yl)-3-(3-(trifluoromethyl)phenyl)urea(compound 3). A mixture of 4-Aminonaphthalene-1-boronic acid pinacolester (31.2 mg, 0.11 mmol) and 3-(Trifluoromethyl)phenyl isocyanate(21.0 μL, 0.31 mmol) in THF (0.9 mL) was stirred over night at roomtemperature. The mixture was concentrated, diluted with dichloromethaneand washed with water. The organic layer was dried over Na2SO4,concentrated in vacuo and the resultant crude product was purified byflash chromatography (20% ethyl acetate in hexanes) to afford 43.6 mg ofcompound 3 (86% yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf=0.4; 1H NMR(300 MHz, MeOD): δ 8.87-8.82 (m, 1H), 8.11-7.91 (m, 4H), 7.67 (d, J=9.0Hz, 1H), 7.60-7.47 (m, 3H), 7.36-7.31 (m, 1H), 1.44 (s, 12H); ESI-MS(m/z): [M]+ calcd. for C24H24BF3N2O3, 456.18; [M+1]+ found, 457.3.N-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)naphthalen-1-yl)-3-(trifluoromethyl)benzamide(compound 4). 4-Aminonaphthalene-1-boronic acid pinacol ester (75.0 mg,0.267 mmol), 3-(Trifluoromethyl)benzoic acid (67.5 mg, 0.348 mmol), HOBt(55.1 mg, 0.348 mmol), EDCI (68.0 mg, 0.348 mmol) and DIPEA (141 μL,0.803 mmol) were dissolved in DMF (790 μL) and stirred overnight at roomtemperature. The crude mixture was diluted in ethyl acetate and washedwith NH4Cl and Na2CO3. The organic layer was dried over Na2SO4 andconcentrated in vacuo. The crude organic product was purified by columnchromatography (20% ethyl acetate in hexanes) to afford 16.6 mg ofcompound 4 (14% yield). TLC (hexanes:EtOAc, 80:20 v/v): Rf=0.4; 1H NMR(300 MHz, MeOD) δ 8.87-8.84 (m, 1H), 8.41-8.36 (m, 2H), 8.13-8.04 (m,2H), 8.01-7.96 (m, 1H), 7.85-7.78 (m, 1H), 7.68 (d, J=6.0 Hz, 1H),7.58-7.55 (m, 2H), 1.47 (s, 12H); ESI-MS (m/z): [M]+ calcd. forC24H23BF3NO3, 441.17; [M+1]+ found, 442.2.8-chloro-1-iodo-3-isopropylimidazo[1,5-a]pyrazine (compound 5). Compound5 was synthesized according to previously published procedure.1-iodo-3-isopropyl-N-methylimidazo[1,5-a]pyrazin-8-amine (compound 6).Compound 5 (21.8 mg, 0.068 mmol) was dissolved in a solution of 40%MeNH2 in MeOH (91 μL) and was stirred at 80° C. for 2 h in a microwave.The reaction mixture was concentrated in vacuo to obtain 20.3 mg ofcompound 6 (94% yield). TLC (hexanes:EtOAc, 50:50 v/v): Rf=0.2; 1H NMR1H NMR (300 MHz, MeOD) δ 7.51 (d, J=6.0 Hz, 1H), 7.04 (d, J=6.0 Hz, 1H),3.42-3.34 (m, 1H), 3.07 (s, 3H), 1.37 (d, J=6.0 Hz, 6H); ESI-MS (m/z):[M]+ calcd. for C10H13IN4, 316.02; [M+1]+ found, 317.1.

1-(4-(8-amino-3-isopropylimidazo[1,5-a]pyrazin-1-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)urea(KIRA2). A mixture of compound 1 (22.1 mg, 0.073 mmol), compound 2 (35.5mg, 0.087 mmol), tetrakis(triphenylphosphine)palladium (2.6 mg, 2.1μmol) and sodium carbonate (17.0 mg, 0.161 mmol) was dissolved in a 3:1mixture of DME/water (280 uL). The mixture was heated overnight at 85°C. The crude mixture was then allowed to cooled to room temperature,diluted in a mixture of acetonitrile/water and purified by reverse phasechromatography (HPLC) to obtain 11.5 mg of KIRA2 (35% yield). TLC(CH2Cl2:MeOH, 95:5 v/v): Rf=0.5; 1H NMR (300 MHz, MeOD): δ 7.95 (s, 1H),7.68-7.64 (m, 1H), 7.65-7.63 (m, 2H), 7.60-7.56 (m, 2H), 7.55-7.48 (m,2H), 7.34-7.31 (m, 1H), 7.02-7.00 (dd, J=6.0 Hz, J=3.0 Hz, 1H),3.49-3.43 (m, 1H), 1.44 (d, J=6.0 Hz, 6H); ESI-MS (m/z): [M]+ calcd. forC23H21F3N6O, 454.17; [M+1]+ found, 455.5. HPLC Purification Conditions:C18 column (250×21 mm), CH3CN/H2O—0.1% CF3CO2H=1:99 to 100:0 over 78min; 8 mL/min; 220 nm and 254 nm detection for 78 min. The purity of GP117 was determined to be >98% by analytical HPLC in two differentsolvent systems.

1-(4-(8-amino-3-isopropylimidazo[1,5-a]pyrazin-1-yl)naphthalen-1-yl)-3-(3-(trifluoromethyl)phenyl)urea(KIRA3). A mixture of compound 1 (12.0 mg, 0.040 mmol), compound 3 (21.9mg, 0.048 mmol), tetrakis(triphenylphosphine)palladium (1.4 mg, 1.2μmol) and sodium carbonate (9.3 mg, 0.088 mmol) was dissolved in a 3:1mixture of DME/water (160 uL). The mixture was heated overnight at 85°C. The crude mixture was cooled to room temperature, diluted in amixture of acetonitrile/water and purified by reverse phasechromatography (HPLC) to obtain 12.3 mg of GP146 (61% yield). TLC(CH2Cl2:MeOH, 95:5 v/v): Rf=0.4; 1H NMR (300 MHz, MeOD): δ 8.27-8.22 (m,1H), 8.02-7.96 (m, 2H), 7.90-7.86 (m, 1H), 7.83-7.79 (m, 1H), 7.72-7.49(m, 5H), 7.37-7.32 (m, 1H), 7.04-6.99 (m, 1H), 3.66-3.55 (m, 1H),1.54-1.48 (m, 6H); 13C NMR (500 MHz, MeOD): δ 154.9, 151.6, 149.8,140.2, 135.9, 132.9, 129.4, 128.7, 128.7, 127.1, 126.6, 126.6, 125.8,125.7, 121.9, 121.9, 121.8, 120.2, 118.7, 118.7, 115.1, 114.6, 112.9,108.4, 25.8, 19.6; [M+1]+ found, 505.4. HPLC Purification Conditions:C18 column (250×21 mm), CH3CN/H2O—0.1% CF3CO2H=1:99 to 100:0 over 78min; 8 mL/min; 220 nm and 254 nm detection for 78 min. The purity ofGP146 was determined to be >98% by analytical HPLC in two differentsolvent systems.

1-(4-(3-isopropyl-8-(methylamino)imidazo[1,5-a]pyrazin-1-yl)naphthalen-1-yl)-3-(3-(trifluoromethyl)phenyl)urea(GP146(NMe)). A mixture of compound 6 (11.1 mg, 0.035 mmol), compound 3(19.3 mg, 0.042 mmol), Tetrakis(triphenylphosphine)palladium (1.3 mg,1.0 umol) and sodium carbonate (8.2 mg, 0.08 mmol) was dissolved in a3:1 mixture of DME/water (130 uL). The mixture was heated overnight at85° C. The crude mixture was cooled to room temperature, diluted in amixture of acetonitrile/water and purified by reverse phasechromatography (HPLC) to obtain 5.0 mg of the GP146(NMe) (27% yield).TLC (CH2Cl2:MeOH, 95:5 v/v): Rf=0.6; 1H NMR (300 MHz, MeOD) δ 8.26 (d,J=9.0 Hz, 1H), 8.03 (s, 1H), 7.96 (d, J=9.0, 1H), 7.90 (d, J=6.0 Hz,1H), 7.84 (d, J=9.0 Hz, 1H), 7.72-7.66 (m, 3H), 7.62-7.51 (m, 2H),7.37-7.34 (m, 1H), 7.04 (d, J=6.0 Hz, 1H), 3.66-3.57 (m, 1H), 2.99 (s,3H), 1.50 (dd, J=15.0, 6.0 Hz, 6H); 13C NMR (500 MHz, MeOD): δ 154.99,151.22, 148.86, 140.19, 135.97, 133.04, 131.68, 129.36, 128.96, 128.80,128.64, 128.54, 126.97, 126.63, 125.86, 125.80, 121.97, 121.84, 120.45,118.68, 114.99, 114.55, 113.05, 108.47, 28.25, 25.75, 19.60; ESI-MS(m/z): [M]+ calcd. for C28H25F3N6O, 518.2; [M+1]+ found, 519.5. Thepurity of GP146(NMe) was determined to be >98% by analytical HPLC.

N-(4-(8-amino-3-isopropylimidazo[1,5-a]pyrazin-1-yl)naphthalen-1-yl)-3-(trifluoromethyl)benzamide(GP146(Am)). A mixture of compound 1 (9.5 mg, 0.031 mmol), compound 4(16.6 mg, 0.038 mmol), Tetrakis(triphenylphosphine)palladium (1.1 mg,0.94 μmol) and sodium carbonate (7.3 mg, 0.069 mmol) was dissolved in a3:1 mixture of DME/water (120 μL). The mixture was heated overnight at85° C. The crude mixture was cooled to room temperature, diluted in amixture of acetonitrile/water and purified by reverse phasechromatography (HPLC) to obtain 5.3 mg of GP146(Am) (34% yield). TLC(CH2Cl2:MeOH, 95:5 v/v): Rf=0.5; 1H NMR (300 MHz, MeOD) δ 8.46 (s, 1H),8.42 (d, J=6.0 Hz, 2H), 8.16-8.13 (m, 1H), 8.01-7.98 (m, 1H), 7.86-7.84(m, 1H), 7.81-7.77 (m, 2H), 7.72-7.69 (m, 1H), 7.68-7.62 (m, 2H),7.60-7.54 (m, 1H), 7.06 (d, J=6.0 Hz, 1H), 3.61-3.52 (m, 1H), 1.53-1.46(m, 6H); ESI-MS (m/z): [M]+ calcd. for C27H22F3N5O, 489.18; [M+1]+found, 490.4 The purity of GP146(Am) was determined to be >98% byanalytical HPLC.

1-(4-(8-amino-3-tert-butylimidazo[1,5-a]pyrazin-1-yl)naphthalen-1-yl)-3-(3-(trifluoromethyl)phenyl)urea(KIRA6). A mixture of 1-iodo-3-tertbutylimidazo[1,5-a]pyrazin-8-amine(60.0 mg, 0.120 mmol), 3 (66 mg, 0.15 mmol),tetrakis(triphenylphosphine)palladium (5 mg, 4 μmol) and sodiumcarbonate (928 mg, 0.27 mmol) was dissolved in a 3:1 mixture ofDME/water (0.5 mL). The mixture was heated overnight at 85° C. The crudemixture was cooled to room temperature, diluted in a mixture ofacetonitrile/water and purified by reverse phase chromatography (HPLC)to obtain 53 mg of KIRA6. TLC (CH2Cl2:MeOH, 95:5 v/v): Rf=0.4; 1H NMR(300 MHz, MeOD): δ 8.26 (m, 1H), 8.08-7.99 (m, 2H), 7.90-7.86 (m, 1H),7.83-7.79 (m, 1H), 7.69-7.52 (m, 5H), 7.35 (d, J=7.4 Hz, 1H), 6.98 (m,1H), 1.65 (s, 9H); 13C NMR (126 MHz, MeOD): δ 154.8, 140.2, 135.7,133.0, 132.4, 131.7, 131.6, 131.0, 130.7, 129.4, 128.8, 128.6, 128.5,127.0, 126.6, 125.9, 125.4, 123.2, 121.9, 120.1, 118.7, 115.0, 114.4,110.1, 33.6, 27.3; ESI-MS (m/z): [M]+ calcd. for C28H25F3N6O (M+H+):519.2; found 519.4.

Generate potent and selective reversible type II inhibitors of IRE1α. Asdescribed above, a type II ATP-competitive inhibitor (KIRA3) that caninactivate IRE1α RNase and kinase activities has been identified, invitro and in vivo (Zhang, J. et al. Nature reviews. Cancer 9, 28-39,(2009)). Described herein are efforts to increase the potency andselectivity of these type II inhibitors. Using structure-based drugdesign, KIRA3 was further optimized. Initially, a homology model of theIRE1α ATP-binding site in the DFG-out conformation, will be used toguide analog synthesis, including use of structures of KIRAs bound toon-targets (IRE1α) and off-targets (Src) to refine the inhibitor dockingprotocol. Described herein is the development of irreversible inhibitorsthat target a non-conserved cysteine in IRE1α's activation loop.Described herein is the development of KIRA3 analogs that contain anelectrophile that targets a cysteine predicted to be accessible whenIRE1α is in the DFG-out conformation. Details are described below.

KIRA analog synthesis: The synthetic strategy for generating inhibitorsof general structure Z is shown FIG. 25. Acylation of commerciallyavailable amine Z1 with carboxylic acids (R₁—CO₂H) that have beenactivated with 1,1′-carbonyldiimidazole (CDI) (or activated with EDCI,DMAP), followed by cyclization with POCl₃ generates imidazopyrimidines(Z2) that are substituted at the 1-position (R₁) (Mulvihill, M. J. etal. Bioorg. Med. Chem. 16, 1359-1375 (2008); Mulvihill, M. J. et al.Bioorganic & Medicinal Chemistry Letters 17, 1091-1097 (2007)). Ureasubstituents are introduced at the C-3 position by iodinating thescaffold with NIS, nucleophilic substitution with ammonia in isoproponal(in a sealed reaction vessel) and palladium-mediated Suzuki couplings tourea-containing boronic esters (prepared as shown in the box) (Jin, M.et al. Bioorganic & Medicinal Chemistry Letters 21, 1176-1180 (2011);Wang, J.-X. et al. Org. Lett. 10, 2923-2926 (2008); Board, J. et al.Org. Lett. 11, 5118-5121 (2009)). An alternate synthetic route thatintroduces substituents at the C-3 position (R₂ substituents) withoutusing a metal-mediated cross-coupling can also be used (Mulvihill, M. J.et al. Bioorganic & Medicinal Chemistry Letters 17, 1091-1097 (2007)).Over 40 analogs have been generated using this synthetic methodology.Representative inhibitors are shown in FIG. 26. KIRA6 (R₁=V; R₃=B), amore potent (IC₅₀(RNase)=210 nM; IC₅₀(kinase)=620 nM) analog of KIRA3,is extensively profiled in Aim 2. KIRA7 (R₁=V; R₃=C) is one of the mostpotent KIRA (IC₅₀(RNase)=<30 nM; IC₅₀(kinase)=35 nM) generated to date.

Irreversible KIRAs that target Cys715 in the activation loop. The IRE1αkinase domain possesses a cysteine residue (Cys715) two residuesC-terminal to the DFG motif (FIG. 27). Cys715 is rapidly alkylated withhaloacetamide-containing ICAT reagents, and the rate is increased underKIRA3 (Zhang, J. et al. Nature reviews. Cancer 9, 28-39, (2009)).Modeling suggests that Cys715 is in close proximity to the R₃substituent of the KIRA scaffold when the DFG motif is in the “out”conformation (the conformation the IRE1α ATP-binding site adopts whenbound to KIRAs). Of the 518 kinases in the human kinome, 42 have acysteine residue at an equivalent or adjacent position (Leproult, E. etal. J. Med. Chem. 54, 1347-1355 (2011)). However, chemical proteomicprofiling studies with type II inhibitors suggest that none of these 42kinases, except IRE1α, are able to adopt the DFG-out inactiveconformation (Krishnamurty, R. et al. Nature chemical biology 9, 43-50,(2013); Brigham, J. L. et al. ACS Chem. Biol. 130123155823009).Therefore, it should be possible to selectively target Cys715 with aproperly oriented electrophile displayed from the KIRA scaffold.Representative irreversible KIRAs that are being generated are shown inFIG. 27 (electrophiles will be introduced in the last synthetic step toavoid instability issues during the palladium-mediated cross coupling).A number of highly selective irreversible kinase inhibitors have beendeveloped by targeting non-conserved cysteine residues (Kwarcinski, F.E. et al. ACS Chem. Biol. 7, 1910-1917 (2012); Barouch-Bentov, R. et al.Molecular Cell 33, 43-52 (2009); Zhang, T. et al. Chemistry & Biology19, 140-154 (2012); Zhou, W. et al. Bioorganic & Medicinal ChemistryLetters 21, 638-643 (2011); Zhou, W. et al. Chemistry & Biology 17,285-295 (2010); Zhou, W. et al. Nature 462, 1070-1074 (2009);Serafimova, I. M. et al. Nature Chemical Biology 8, 471-476 (2012);Henise, J. C. & Taunton, J. J. Med. Chem. 54, 4133-4146 (2011); Cohen,M. S. f et al. Science 308, 1318-1321 (2005)).

3. Analysis of the GP146—IRE1α and APY29—IRE1α Interactions.

To further confirm that AYP29 and GP146 are exerting their opposingeffects through the same ATP-binding site, a series of biochemicalfootprinting experiments were conducted (Tu, B. P. & Wang, J. C. Proc.Natl. Acad. Sci. USA 96, 4862-4867 (1999); Underbakke, E. S. et al.Angew. Chem. Int. Ed. 47, 9677-9680 (2008)). Specifically, theaccessibility of three native cysteine residues within human IRE1α(Cys572, Cys645, and Cys715) to alkylating agents in the presence orabsence of APY29 and GP146 was determined (FIG. 3a ). For these studies,electrophilic isotope-coded affinity tag (ICAT) reagents were used toallow a ratiometric and, therefore, quantitative comparison ofalkylation rates (Underbakke, E. S. et al. Angew. Chem. Int. Ed. 47,9677-9680 (2008)). As Cys645 and Cys715 are located within theATP-binding cleft of IRE1α, the accessibility of these residues would beexpected to be affected by ligands that occupy this site, while Cys572is a solvent-exposed residue located on the top of the N-terminal lobeof the kinase. Consistent with both APY29 and GP146 occupying theATP-binding site of IRE1α, Cys645, which is located in the kinase hingeregion, is highly shielded from alkylating agents in the presence ofeither inhibitor (FIG. 3b ). In contrast, these inhibitors exertopposing effects on the accessibility of Cys715, with APY29 slowing therate of alkylation and GP146 increasing it. Cys715 is located in theactivation loop of IRE1α (two residues C-terminal to the DFG-motif) andthe divergent influence of APY29 and GP146 on this residue is concordantwith these ligands stabilizing different conformations of the activationloop (FIG. 3b ). As expected, no detectable difference in theaccessibility of Cys572, which is distal to the kinase active site ofIRE1α, is observed in the presence of either inhibitor.

Next, molecular docking experiments were performed to obtain a betterunderstanding of how GP146 and APY29 interact with the ATP-binding siteof human IRE1α. A model of the DFG-in ATP-binding site conformation wasgenerated from a co-crystal structure of human IRE1α bound to ADP (PDBcode 3P23, chain A) (Ali, M. M. et al. EMBO J. 30, 894-905 (2011)). As astructure of IRE1α in the DFG-out conformation has not yet beendescribed, a homology model of this form was generated by using theactivation loop of another kinase, the tyrosine kinase Abl2, as atemplate. Both the DFG-in and DFG-out models were optimized usingmulti-step all-atom minimization and explicit water molecular dynamics(MD) simulations (Bowers, K. J. et al. in Proceedings of the ACM/IEEEConference on Supercomputing (SC06) (Tampa, Fla., USA, 2006)).Predictably, the docked structure of APY29 bound to the DFG-inconformation of human IRE1α is similar to that of this ligand bound tothe yeast IRE1 enzyme (FIG. 19) (Korennykh, A. V. et al. Nature 457,687-693 (2009)). The pyrazole ring of APY29 forms hydrogen bonds withthe kinase hinge region and the pyrimidine moiety occupies the adeninepocket. Attempts to obtain a favorable pose of APY29 bound to theDFG-out conformation of IRE1α were unsuccessful, which is consistentwith the ability of this ligand to exclusively stabilize the activeconformation of the ATP-binding site.

The most favorable docking pose for GP146 bound to the DFG-outconformation of IRE1α is shown in FIG. 3c . In this pose, thepyrazolopyrimidine ring of this ligand forms two hydrogen bonds with thehinge region and occupies the adenine pocket. The bulky naphthyl ring ofGP146 adopts an almost orthogonal conformation relative to the corescaffold and stacks against the Ile gatekeeper residue. Like other typeII inhibitors, the trifluoromethylphenyl moiety of GP146 occupies thehydrophobic pocket created by movement of the Phe sidechain in theDFG-motif. While GP146 is well accommodated in the DFG-out conformationof human IRE1α, no favorable poses were observed for this inhibitorbound to the DFG-in conformation. Indeed, the docking studies predictthat the only way that GP146 can bind to IRE1α without movement of theDFG motif in the activation loop is if the inhibitor disrupts canonicalinteractions with the hinge region of the kinase.

To further experimentally test the docking model, analogs of GP146 thatcontain structural elements predicted to lower inhibitor potency weregenerated (FIG. 3d ). GP146(NMe) contains an N-methyl group that wouldbe predicted to disrupt its interaction with the hinge region of IRE1α,and the amide linkage of GP146(Am) should not allow thetrifluoromethylphenyl moiety to form as favorable interactions with thehydrophobic pocket created by movement of the DFG-motif. Consistent withthe model, both GP146(NMe) and GP(146Am) show a markedly diminishedability to inhibit the RNase activity of IRE1α compared to GP146 (FIG.3d ).

4. GP146 and APY29 Divergently Affect the Oligomerization State of IRE1α

Increasing concentrations of IRE1α* were incubated with either DMSO, orsaturating concentrations of APY29 or GP146 and the ratio ofoligomeric—defined as all species greater than monomers (mostlydimers)—to monomeric IRE1α was determined (FIG. 4a ). In the absence ofligands, IRE1α* shows a concentration-dependent increase in theoligomer/monomer ratio. The presence of APY29 further enhances—whereasGP146 decreases—this concentration-dependent increase in the IRE1α*oligomer/monomer ratio. Taken together, the in vitro data support amodel in which these two classes of kinase inhibitors divergentlymodulate IRE1α* RNase activity by exerting opposing effects on theoligomerization state of the enzyme (FIG. 4b ).

5. IRE1α* Mutants with an Enlarged ATP-Binding Pocket Show IncreasedSensitivity to GP146

Having used a truncated form of IRE1α for in vitro studies, cell-basedexperiments were used to test whether it would be possible to replicatedivergent modulation of the full-length IRE1α transmembrane protein withthe two classes of kinase inhibitors. The on-target effects of GP146were tested and confirmed using IRE1α chemical-genetic systemspreviously developed (Han, D. et al. Cell 138, 562-575, (2009)).Specifically, tetracycline-inducible isogenic T-REx 293 stable celllines expressing either WT or a “holed” IRE1α gatekeeper mutant^(I642A)were used to determine whether GP146 is able to block the RNase activityof IRE1α in vivo. Induced with doxycycline (Dox), the transgenicWT-IRE1α or IRE1α^(I642A) spontaneously cluster in the ER,trans-autophosphorylate and splice XBP1 mRNA, without requiring upstreamER stress (FIG. 5a and FIG. 20). As expected, GP146 inhibitsautophosphorylation and XBP1 mRNA splicing in the WT cell lines (FIGS.20a and 20b ). Consistent with these inhibitory effects occurringthrough a direct interaction with IRE1α, control compound GP146(NMe)does not affect either of these parameters, even at the highestconcentration tested (FIG. 20c ). Furthermore, it was hypothesized thatthe enlarged ATP-binding pocket of IRE1α^(I642A) would betteraccommodate the bulky C-3 substituent of GP146, leading to enhancedsensitivity. Indeed, the docking studies suggest that the naphthyl ringof GP146 is able to occupy a hydrophobic pocket that is accessible inIRE1α^(I642A) and not the wild type protein (FIG. 21). Confirming thisnotion, low nanomolar concentrations of GP146 are sufficient tocompletely block autophosphorylation and XBP1 splicing through thismutant (FIGS. 5a and 5b ). Furthermore, increasing concentrations of thetype I “bumped” inhibitor 1NM-PP1, which is selective for mutant kinasesthat contain Ala or Gly gatekeeper residues, is able to rescue the RNaseactivity of IRE1α^(642A) in the presence of GP146 (FIG. 5c ).

The data illustrates a model for IRE1α^(I642A) which can be activatedmerely through overexpression to basally splice ˜50% of cellular XBP1mRNA, that 1NM-PP1 further increases—while GP146 reduces—the activity ofthe RNase (FIG. 5d ). These divergent effects proceed from thestabilization of the kinase active site in two distinct modes by theseinhibitors, with 1NM-PP1 acting on the “holed” IRE1α^(I642A) kinase in asimilar fashion as APY29 does for WT IRE1α. In summary, the type IIpharmacophore GP146 likely enforces an inactive kinase conformation inIRE1α^(1642A), and as it does with WT IRE1α.

6. GP146 Blocks Both the Autophosphorylation and RNase Activities ofEndogenous IRE1α In Vivo

To further explore how IRE1α modulators affect the kinase and RNaseactivities of endogenous IRE1α under ER stress, in vivo studies usingINS-1 rat insulinoma cell lines, which are derived frominsulin-producing pancreatic β-cell tumors and contain largewell-developed ERs, were conducted. These cells were treated with the ERSERCA ATPase pump inhibitor, thapsigargin (Tg), to induce ER stress andIRE1α activation at levels causing ˜50% splicing of cellular XBP1 mRNA(FIG. 6a ). Recapitulating the in vitro results, GP146 and APY29demonstrate opposing dose-dependent effects on ER stress-inducedactivation of the RNase of endogenous IRE1α (FIG. 6a ). Furthermore,GP146 abrogates IRE1α autophosphorylation at a similar concentration asit blocks RNase activity (FIGS. 6b and 6c ). Control compound GP146(NMe)does not block the splicing of XBP1 mRNA (FIG. 6d ). Consistent with itsin vitro activity, the type I inhibitor sunitinib is able to partiallyinhibit the kinase activity of IRE1α, but has no effect on the RNaseactivity of this enzyme (FIGS. 6b and 6c ) at the concentrations tested.The RNase inhibitor STF-083010 was also tested in INS-1 cells that hadbeen treated with Tg. As expected, this compound inhibits XBP1 splicingin a dose-dependent manner, but does not prevent IRE1αauto-phosphorylation (FIGS. 6b and 6c ). Therefore, GP146 is the onlycompound identified to date that has the ability to block both enzymaticactivities of IRE1α, both in vitro and in vivo (FIG. 6e ).

7. Expression and Purification of IRE1α* and dP-IRE1α*.

A construct containing the cytosolic kinase and RNase domains of humanIRE1α (residues 469-977, IRE1α*) was expressed in SF9 insect cells byusing Bac-to-Bac baculovirus expression system (Invitrogen) with a6-His-tag at the N-terminus, and purified with a Ni-NTA (Qiagen) column.To generate dP-IRE1α*, basal phosphorylation sites were removed byincubating IRE1α* with λ-PPase (NEB) at a molar ratio of 5:1 (IRE1α*:λ-PPase) in 50 mM HEPES pH 7.5, 100 mM NaCl, 1 mM MnCl2, 2 mM DTT, 0.01%Brij 35 for 40 min at RT. Dephosphorylation was verified byimmunoblotting with an anti-phosphoIRE1α antibody.

8. In Vitro Characterization of Compounds (IRE1α*)

KIRAs are tested for ability to inhibit IRE1α* kinase and RNaseactivities in vitro. The XBP1 minisubstrate assay shown in FIG. 1B-1D,is amenable to 96- or 384-well format, and is used to determine RNaseIC₅₀s. In parallel, kinase IC₅₀s for all KIRAs are determined in a96-well dot blot assay with 32γ-ATP and STK peptide substrate 2 assubstrates. Time-dependence of inhibition is determined for allelectrophile-containing KIRAs. RNase and kinase assays have been used toprofile the KIRAs in FIG. 26, showing a strong correlation betweenkinase and RNase IC₅₀s. The most potent KIRAs are tested in an IRE1α*autophosphorylation assay. Compounds that exhibit an IC₅₀(RNase)<200 nMare counter-screened against a panel of kinases that are likelyoff-targets (Src, Abl, p38α), affect cell fate (mTor, IKKβ),down-regulate protein translation (PKR, PERK, GCN2, HRI), aredown-stream targets of IRE1 signaling (Jnk1/2, MKK4, MKK7), and arerepresentative of the entire kinome (AurA, Erk2, Cdk2, EGFR, FAK,MAP3K5, PKA). The profiling data obtained from these screens are used todesign more selective KIRAs. KIRA3 and KIRA6 have been tested against 12kinases in this panel and the only off-target inhibition observed is forthe tyrosine kinases Src and Abl. Thus, the structure-based designstrategy uses these two kinases as counter targets (described below).

9. Kinase Assays.

Inhibitors (initial concentration=80 μM, 2-fold serial dilutions) wereincubated with IRE1α* in cleavage buffer (20 mM Hepes at pH 7.5, 0.05%Triton X100, 50 mM KOAC, 1 mM Mg(OAC)₂, 1 mM DTT) for 20 min, followedby incubation with 10 μCi [γ-³²P]ATP (3000 Ci/mmol, Perkin Elmer) at RTfor 30 min. Samples were then separated by SDS-PAGE, andautoradiographed. The auto-phosphorylation level were quantified bysetting the band intensity of RE1α* without compound treatment as 1 andthe background as 0.

10. In Vitro RNase Assay.

5′FAM-3′BHQ-labeled XBP1 single stem-loop minisubstrate(5′FAM-CUGAGUCCGCAGCACUCAG-3′BHQ) was purchased from Dharmacon. 0.2 μMIRE1α* or dP-IRE1α* were incubated with inhibitors or DMSO for 20 min incleavage buffer, followed by incubation with 3 μM RNA substrate for 5min. The reaction was quenched by adding urea to a final concentrationof 4 M, and the fluorescence was detected on a SpectraMax M5 microplatereader (Molecular Devices) with excitation and emission wavelengths of494 nm and 525 nm, respectively. The fluorescence intensities werenormalized by setting the signal for the reaction with IRE1α* and DMSOto 1 and the reaction without IRE1α* to 0. The cleavage products werealso resolved by urea PAGE after phenol/chloroform extraction andethanol precipitation. Internally ³²P-labelled mouse XBP1 RNA was alsoused as a substrate, as described (Han, D. et al. Cell 138, 562-575,(2009)).

11. ICAT Footprinting.

Heavy and light iodonated ICAT reagents were made as previouslydescribed (Underbakke, E. S. et al. Angew. Chem. Int. Ed. 47, 9677-9680(2008)). Purified human Ire1α was exchanged into 50 mM Tris (pH 8.0), 50mM KCl, 5 mM MgCl2, and 0.5 mM TCEP. One 3 μM stock solution was dividedinto three solutions, and each was mixed with either DMSO, APY29, orGP146 to yield solutions containing 1% DMSO and 20 μM of inhibitor.Heavy labeling reagent was added to the protein solutions, and 25 μLaliquots were taken at specified times and quenched with excess DTT.Samples were precipitated with 0.2% sodium deoxycholate and 10%trichloroacetic acid on ice for 10 min. The mixtures were centrifuged at4° C. for 15 min, and pellets were washed with cold acetone. The pelletswere then resuspended in 30 μL of 200 mM Tris (pH 8.0), 7 M urea, and2.4 mM light labeling reagent, and incubated in the dark for 30 min. Thesolutions were diluted with 210 μL 200 mM Tris (pH 8.0), 5.7 mM CaCl₂),0.5 μg porcine trypsin (TPCK treated, Sigma), and 125 ng GluC (Roche),and incubated at room temperature overnight. Samples (0.3 μmol) wereinjected onto a Thermo Scientific Dionex Acclaim Pepmap100 NanoLCcapillary column (Cis, 150 mm length, I.D. 75 pm, 3 pm particle size)connected inline to a Finnigan LCQ mass spectrometer. Peptides ofinterest were identified by MS/MS data (Sequest), and corresponding XICpeaks were integrated. Alkylation curves were fit using GraphPad Prismsoftware (Binding—Kinetics, Dissociation—One-phase exponential decay).

12. Molecular Modeling.

Molecular modeling of KIRA interactions with the ATP-binding site ofIRE1α. To gain insight into how KIRA3 and KIRA6 interact with the IRE1αATP-binding site, molecular modeling experiments were used. A model ofthe DFG-in ATP-binding site conformation was generated from a co-crystalstructure of human IRE1α bound to ADP. As a structure of IRE1α in theDFG-out conformation has not yet been described, a homology model ofthis form was generated by using the activation loop of another kinase,the tyrosine kinase Abl2, as a template. Both the DFG-in and DFG-outmodels were optimized using multi-step all-atom minimization andexplicit water molecular dynamics (MD) simulations. Consistent with theobserved SAR and type II pharmacophores of KIRA3 and KIRA6, theseligands are only accommodated in the ATP-binding site of IRE1α when theDFG-motif is in the “out” conformation (DFG-out). Furthermore, the mostfavorable docking poses for both KIRA3 and KIRA6 involve both of theseligands making all of the canonical contacts of type II inhibitors.Using this model, the predicted docking scores for the KIRAs shown inFIG. 3c are very consistent with in vitro kinase and RNase inhibitionresults. For example, KIRA7 (R₁=V; R₃=C: IC₅₀(RNase)=<30 nM;IC₅₀(kinase)=35 nM) and KIRA6 (R₁=V; R₃=B: IC₅₀(RNase)=210 nM;IC₅₀(kinase)=620 nM) have significantly and slightly more favorableGlide_SP and MMGBSA scores than KIRA3, respectively. Furthermore, thismodel has been used to design inactive KIRA3 analogs for controls incellular assays. Currently, the model for the IRE1α“DFG-out” inactiveconformation is used to filter potential analog syntheses based upontheir docking scores.

The DFG-in structure of IRE1α was generated from a co-crystal structureof human IRE1α bound to ADP (PDB code 3P23, chain A) (Ali, M. M. et al.EMBO J. 30, 894-905 (2011)). The structure was prepared using theprotein preparation workflow in Maestro (Schrodinger) to assignhydrogens, optimize hydrogen bonds, and to perform constraintminimization (impref). The homology model of IRE1α in the DFG-outconformation was built using the activation loop of a DFG-out templatekinase (Abl2; PDB code 3GVU) (SEQ ID NO:6) (Salah, E. et al. J. Med.Chem. 54, 2359-2367 (2011)) in Prime (Schrodinger). The initial DFG-outmodel was optimized using the protein preparation workflow describedabove. Both DFG-in and DFG-out models were then optimized using amulti-step all-atom minimization and molecular dynamics (MD) simulationimplemented in the software package Desmond (DE Shaw Research) (Bowers,K. J. et al. in Proceedings of the ACM/IEEE Conference on Supercomputing(SC06) (Tampa, Fla., USA, 2006)). Optimizations were run using theOPLS-AA force field, the TIP4P explicit solvent model in an orthorhombicsimulation box 10 Å distance in all directions and adding counter ions.Simulations were performed at 300 K and 1.01325 bar using the NPTensemble class. All other settings were default. The productionsimulation time was 12 ns. Simulations were run on an IBM E-server 1350cluster (36 nodes of 8 Xeon 2.3 GHZ cores and 12 GB of memory). Severallater simulation frames were extracted from the DFG-in and DFG-outsimulations based on conformational diversity and low (stable) RMSD.These frames were then used to generate the DFG-in and DFG-out models ofIRE1α^(I642A). To avoid side chain clashes, constraint (impref)minimization (in Maestro, Schrodinger) was performed for the WT andI642A structures of IRE1α. These structures were then used for furthermodeling.

Using the optimized DFG-in and DFG-out structures of WT andIRE1α^(I642A) described above, initial binding poses for APY29 and GP146were generated as follows. Ligands were prepared using ligprep(Schrodinger Inc.) to generate ionization states (pH=7) andstereoisomers resulting in two representations for GP146 and four forAPY29. Ligands were initially docked into the DFG-in and DFG-out modelsof IRE1α using the Induced Fit Docking (IFD) (Schrodinger Inc.) protocolwith default settings. The IFD protocol includes a constraint receptorminimization step followed by initial flexible Glide docking of theligand using a softened potential to generate an ensemble of poses. Foreach pose, the nearby receptor structure was then refined using Prime.Each ligand was then re-docked (using Glide) into its correspondingoptimized low-energy receptor structure and ranked by Glide score. Thebest pose with highest IFD score obtained for each ligand was againsubjected to MD simulation (8-10 ns production runs) for furtheroptimization of the protein ligand complex. The MD protocol includes amulti-step procedure for minimizations and short MD runs followed by theproduction MD simulation. Ligand poses were observed to be stable duringthe production MD runs. The final frames of these simulations were thenused for ligand docking after constraint (impref) minimization (Maestro,Schrodinger Inc.). The best pose for each ligand was selected based onthe Glide score, known interactions and visual inspection. The 3D plotsof ligand poses were produced using PyMol.

13. IRE1α* Cross-Linking to Determine Oligomer to Monomer Ratio.

Structural analysis of IRE1-KIRA and off-target kinase-KIRA complexes:For KIRAs that show sufficient potency and selectivity, furtherbiochemical and biophysical characterization are performed. It isdetermined if new KIRA analogs are able to prevent thedimerization/oligomerization of IRE1α using the crosslinking strategyshown in FIGS. 4 and 30. KIRA6, like KIRA3, stabilizes the monomericstate of IRE1α. Analytical ultra-centrifugation (AUC) is used to furtherconfirm that KIRAs stabilize the monomeric form of IRE1α 49. Crystalstructures of the most promising KIRAs bound to IRE1α and the off-targetkinase Src are being obtained. These structures are used to refine thedocking protocols for IRE1α, which aid computational design ofinhibitors with increased potency. Structures of KIRA-Src complexes areused to identify interactions that are unique to IRE1α and inform thedesign of KIRAs that possess increased selectivity. On-target/off-targetstructural strategy has been used to develop highly potent and selectiveinhibitors of Toxoplasma gondii and Cryptosporidium parvum CDPK1(Murphy, R. C. et al. ACS Med. Chem. Lett. 1, 331-335 (2010); Larson, E.T. et al. J. Med. Chem. 55, 2803-2810 (2012); Johnson, S. M. et al. JMed. Chem. 55, 2416-2426 (2012); Ojo, K. K. et al. J. Cin. Invest. 122,2301-2305 (2012)). Diffraction-quality crystals of Src bound to KIRA3have been obatined. A structure of human IRE1α bound to ADP has beenreported⁴⁸. Using the same IRE1α expression construct, and purificationprotocol multi-milligram quantities of homogenous unphosphorylated IRE1αhave been obtained. This protein is currently being used by to screenfor diffraction quality crystals of IRE1α-KIRA3 and IRE1α-KIRA6complexes, and initial screening results are very promising.

Increasing concentrations of IRE1α* (0.49-30 μM) were incubated withDMSO, GP146 (200 μM), or APY29 (200 μM) for 20 min, then cross-linked byadding 250 μM disuccinimidyl suberate (DSS) (Pierce) for 1 hr at RT incleavage buffer. The reaction was quenched by addition of 50 mM Tris-HCl(pH 7.5). The samples were then boiled, resolved on SDS-PAGE, andimmunoblotted for IRE1α with an anti-IRE1α antibody, (visualization andquantification with a LI-COR Odyssey scanner).

Cell culture and XBP1 mRNA splicing. INS-1 cells were grown in RPMI, 10%fetal calf serum, 1 mM sodium pyruvate, 10 mM HEPES, Pen/strep, 2 mMglutamine and 50 mM β-mercaptoethanol. T-REx 293 IRE1α or IRE1α^(I642A)were grown in DME H-21 with 10% fetal calf serum and Pen/strep. After 1hr incubation with compounds, INS-1 cells were treated with 6 nMthapsigargin for 4 hrs, and T-Rex 293 IRE1α-expressing cells weretreated with 1 μM Dox for 8 hrs. The RNA was then extracted using RNeasyMini Kit (Qiagen), and reverse transcribed using the QuantiTect ReverseTranscription Kit (Qiagen). XBP1 splicing was performed as previouslydescribed⁷. Primers used: sense primer rXBP 1.35(5′-AAACAGAGTAGCAGCACAGACTGC-3″) (SEQ ID NO:7) and antisense primer rXBP1.2AS (5′-GGATCTCTAAGACTAGAGGCTTGGTG-3′) (SEQ ID NO:8) for INS-1 cellline, while sense primer mXBP1.3S (5′-AAACAGAGTAGCAGCGCAGACTGC-3′) (SEQID NO:9) and antisense primer mXBP1.2AS(5′-GGATCTCTAAAACTAGAGGCTTGGTG-3′) (SEQ ID NO:10) for T-Rex 293 cellline. PCR products were resolved on 2.5% agarose gels, stained withEtBr, and quantified by ImageJ.

Immunoblot analysis. INS-1 cells were incubated with compounds or DMSOfor 1 hr, followed by 1 μM Tg for 2 hrs. T-Rex 293 IRE1α-expressingcells were incubated with compounds or DMSO for 1 hr and then treatedwith 1 μM Dox for 8 hrs. Cells were lysed in RIPA buffer (20 mMTris-HCl, pH 7.5, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate, 150mM NaCl, 1 mM EDTA, 1% NP-40, complete EDTA-free protease inhibitor(Roche) and phosphatase inhibitor cocktail (Sigma)), and cleared lysateswere subjected to SDS-PAGE and transferred to nitrocellulose. Blocking,antibody incubation, and washing were done in PBS or TBS with 0.05%Tween-20 (v/v) and 5% (w/v) non-fat dry milk or BSA, or blocking buffer(Odyssey). Primary antibodies were diluted: IRE1α (1:1000) (Santa CruzBiotechnology), phospho-IRE1α (1:1000) (Novus Biologicals), GAPDH(1:3000) (Santa Cruz Biotechnology), Myc (1:4000) (Santa CruzBiotechnology). The antibody binding was detected by usingnear-infrared-dye-conjugated secondary antibodies and visualized on theLI-COR Odyssey scanner.

As described herein, IRE1α* means a recombinant human (rh) IRE1α. rhIRE1α has the human IRE1a (469-977) sequence: SEQ IDNO:1 (w/his tag);and SEQ ID NO:2 (w/o his tag).

14. Determine Whether Blocking the Terminal UPR with IRE1α* KinaseInhibitors Prevents ER Stress-Induced β-Cell Degeneration. On-TargetEffects of KIRAs, Underlying Mechanisms, and Amelioration of Beta CellDeath and Preservation of Function Under ER Stress by KIRA6

Inhibiting IRE1α's RNase activity using KIRAs shuts down endonucleolyticdecay of mRNAs localizing to the ER membrane. ER-localized mRNA decayhas been directly linked to the terminal UPR. One model holds thatdepletion of key mRNAs encoding factors needed to maintain ER structuraland functional integrity (e.g. ER chaperones) may underlie apoptoticeffects. IRE1α RNase targets select microRNA (miR) precursors toterminate their biogenesis. These mature miRs normally exert inhibitoryeffects on gene expression of key pro-apoptotic targets; e.g., depletionof four select miRs leads to: (i) translational derepression of theapoptosis initiator caspase 2, and (ii) stabilization of the mRNAencoding pro-oxidant thioredoxin-interacting protein (TXNIP). Usingengineered chemical-genetic systems is elucidating these mechanisticsignature events of IRE1α RNase-induced cell death, and helping tounderstand the physiological consequences of inhibiting IRE1α RNaseactivity by KIRAs.

15. Duration and Magnitude of ER Stress Determine Entry into theTerminal UPR Through High-Order Oligomerization and Hyperactivation ofIRE1α Kinase/RNase Catalytic Domains.

To rigorously test for cytoprotective effects, thresholds of ER stresswere dilenated that when crossed push cells into apoptosis. Using ratinsulinoma (INS-1) cells that have a well-developed ER and secreteinsulin, the duration and magnitude of ER stress that triggers apoptosiswere quantified. Two variables—concentration of ER stress inducer (e.g.Thapsigargin—Tg) and time of exposure to the agent—are directly linkedto the percentage of cells entering apoptosis (FIGS. 28, A and B). Suchregimes can be defined for other ER stress inducers such as theglycosylation inhibitor, tunicamycin (Tm) (FIG. 28,C). Increasing ERstress causes progressive increases in endogenous IRE1α phosphorylation,increases in XBP1 mRNA splicing (FIG. 28, E), depletion throughendonucleolytic decay of the ER-localized mRNA, Ins1, which encodesproinsulin (FIG. 28, F), and induction of the pro-apoptotictranscription factor, CHOP (FIG. 28, G).

These aforementioned terminal UPR signaling events can be completelymimicked simply by controlled over-expression of IRE1α, in the completeabsence of upstream ER stress. Tetracycline-inducible isogenic INS-1stable cell lines expressing WT IRE1α were generated. Induced withdoxycycline (dox) the transgenic IRE1α proteins oligomerize,spontaneously trans-autophosphorylate and trigger XBP1 mRNA splicing(FIGS. 29, A and B). The transgenic systems are finely tunable, withincreasing [Dox] causing progressively greater IRE1α induction (thetransgenic IRE1α protein is Myc-tagged). Phospho/Myc IRE1α ratios arefinely controllable (and measureable) with increasing [Dox], as is XBP1mRNA splicing. Mimicking dose-dependency by ER stress agents into aterminal UPR, increasing [Dox] spontaneously triggers entry into aterminal UPR by causing IRE1α kinase hyper-phosphorylation and RNasehyperactivation past a critical threshold and induction of key signatureevents of the terminal UPR (FIG. 29, C). These include reduction ofmiR-17 (FIG. 29, D) and Ins1 mRNA, induction of CHOP mRNA (FIG. 29, E),induction and proteolytic cleavage of caspases 1, 2, and 3 (FIG. 29, F),and apoptosis as measured by Annexin-V staining (FIG. 29, G).

KIRAs break high-order oligomerization of IRE1α kinase domains,attenuate RNAse activity, and reduce entry of cells into the TerminalUPR. In exciting preliminary data, all these terminal UPR endpoints arecurtailed by pre-treating cells with KIRA6, before exposing them to ERstress inducers. in vitro, KIRA6 inhibits IRE1α* RNase and kinaseactivities with similar IC₅₀s (FIGS. 30, B and C). in vivo, KIRA6inhibits endogenous IRE1α auto-phosphorylation in a dose-dependentmanner (FIG. 30, D); in contrast the aldehyde-based IRE1αRNase-inhibitor, STF, does not inhibit IRE1α auto-phosphorylation, nordoes a control compound KIRA6(in).

Furthermore, in vitro, KIRA6 reduces concentration-dependentoligomerization of IRE1α* (FIG. 30, E). in vivo, KIRA6 inhibitsendogenous IRE1α-mediated XBP1 mRNA splicing provoked by Tm (FIG. 30,F). Intriguingly, KIRA6 inhibits ER-localized endonucleolytic decay ofIns1 mRNA at lower doses of the drug than needed to inhibit XBP1 mRNAsplicing (FIG. 30, G); this discriminatory effect may occur becausehigher-order oligomers are needed to catalyze Ins1 mRNA decay, whereasdimers suffice for XBP1 mRNA splicing. Because ER-localizedendonucleolytic mRNA decay promotes apoptosis—in contrast to XBP1 mRNAsplicing, which promotes adaptation—this differential effect of KIRAsreveals the existence of a natural “therapeutic window” which reducesentry of INS1-1 cells into apoptosis (FIG. 30, H). These cytoprotectiveeffects of KIRA6 extend to myriad cell types, including freshlyharvested pancreatic islets from C57/BL6 mice treated with Tm (FIG. 30,I). KIRA6 cytoprotective effects are dependent on IRE1α because they areabsent in Ire1α^(−/−) mouse embryonic fibroblasts (MEFs), but stilldemonstrable in WT and Xbp1^(−/−) MEFs (FIG. 30, J). A model ofKIRA6-mediated cytoprotection is shown (FIG. 30, J); it posits that thetype II kinase inhibitor, KIRA6, reduces kinase/RNAsehomo-oligomerization on the cytosolic face of IRE1α, which consequentlyreduces RNase hyperactivity under ER stress, preventing pro-apoptoticER-localized mRNA decay and granting cells extended reprieve fromprogrammed cell death.

16. UPR and Diabetes

β-cells from mouse and human islets exposed to irremediably high ERstress will show activation of many of the terminal UPR endpointsdescribed herein. Besides the ER-localized mRNAs and select micro RNAsso far identified as IRE1α substrates, other miRs and small non-codingRNAs remain to be discovered and related changes will constitute aTerminal UPR signature that can be followed as therapeutic endpoints foramelioration by KIRAs.

Described herein is the characterization of four select miRs that decayin vivo upon IRE1α hyperactivation. These are miR-17, miR-34a, miR-96,and miR-125b. WT-IRE1α* directly cleaved pre-miR-17 in vitro at sitesdistinct from those cleaved by DICER, as mapped by primer extension. Thescission sites of pre-miR-17 are identical to those of XBP1mRNA—(G/C)—and diverge at the flanking regions. Thus, by reducing levelsof pre-miRs, IRE1α antagonizes DICER action to reduce cellular levels ofthe corresponding mature miRs. Intriguingly, IRE1α* (I642G), which canbe activated by 1NM-PP1 to cleave XBP1 mRNA in vitro, can also cleavepre-miR-17 under 1NM-PP1. An RNAse mutant, IRE1α (N906A), is compromisedfor cleavage of pre-miR-17 (FIG. 31, A-C). This provokes the hypothesisthat IRE1α is capable of exhibiting extra-XBP1 mRNA endonucleolyticactivity in a graded fashion. As IRE1α homo-oligomerizes in the ERmembrane in proportion to the concentration of unfolded proteins in theER lumen, it progressively trans-autophosphorylates. Furthermore, saltbridges between phospho-amino acid groups and other residues reinforcehigher-order homo-oligomerization of kinase/RNAse domains, as was shownusing yeast IRE1. Thus, as IRE1α protein clusters into higher-orderoligomers, it acquires increasing activity towards its RNA substrates.The most efficient substrate is XBP1 mRNA, followed by select pre-miRs(e.g. 17, 34a, 96, and 125b), then followed by the ER-localized mRNAsubstrate, Ins1.

By breaking higher-order IRE1α oligomers with KIRAs, many miR targetswill be preserved at levels found in unstressed cells. As the four miRsfound to exert inhibitory effects on post-transcriptional generegulation of caspase 2 and the NLRP3 inflammasome activator, TXNIP,KIRA6 will reduce levels of these amplifiers of ER stress, even thoughunfolded proteins still persist in the ER lumen. Preliminary data areconsistent with these predictions. It is an interesting possibility thatit is not unfolded proteins in the ER per se that compromise cellfunction and lead to programmed cell death, but instead active terminalUPR signaling through IRE1α RNase hyperactivation. Thus, IRE1α KIRAsshould reduce oligomerization by reinforcing the DFG-out, inactiveATP-binding site conformation, and consequently reduce RNase activity todecrease ER stress-induced cell death. As a corollary, type I kinaseinhibitors, such as 1NM-PP1, should increase oligomerization byreinforcing the DFG-in, active ATP-binding site conformation, andconsequently increase RNase activity to increase ER stress-induced celldeath.

Type I kinase inhibitors antagonize the effects of type II kinaseinhibitors (KIRAs) to promote cell death under ER stress. FIG. 32 showsdata consistent with this notion. KIRAs should ameliorate terminal UPRendpoints promoted by 1NM-PP1 in the context of the IRE1α (I642G)cellular chemical genetic systems under ER stress: Ins1 and 2 mRNAdecay, miR-17, 34a, 96, and 125b decay, Caspase 1, 2, and 3 cleavage,TXNIP mRNA stabilization and translation, and consequent IL-10maturation and secretion. Measurement of cell death endpoints (Annexin-Vstaining) are being made in the engineered cell systems as a function ofthe competing effects of 1NM-PP1 and KIRAs. As a prelude to testing inin vivo mouse models, is testing of all terminal UPR endpoints, with andwithout KIRA6, in freshly-harvested murine (C57BL/6) islets subjected toexogenous ER stress agents, as well as islets from two spontaneousmodels of diabetes: the Ins2(C96Y)—“Akita”—diabetic mouse andoverexpression of IRE1α in islets.

17. Characterization of KIRAs

Potent and selective IRE1α inhibitors are being tested for their generaltoxicity against human cultured cell lines. For compounds that lacktoxicity, the ADME, pharmacokinetic and toxicological properties arebeing determined. Compounds with favorable PK/ADMET properties aretested for efficacy in two mouse diabetic models—the proinsulin foldingmutant, Akita, and overexpression of IRE1α in murine islets.

Cytotoxicity testing: Any KIRAs that show sub-micromolar potency in thecellular models described above are subjected to cytotoxicity assaysagainst seven mammalian cell lines. These assays are helpful inpredicting any general or tissue specific toxicity that may occur whenKIRAs are administered to animals. KIRAs are tested against thefollowing seven cell lines: L1210 (mouse lymphoblasts), W1-L2 (humanlymphoblasts), HT-1080 (human fibrosarcoma), SF-539 (humanglioblastoma), NCI-H460 (human large cell lung carcinoma), HCC-2998(human colon carcinoma), and HL-60 (human promyelocytes). This panelprovides sufficient diversity to predict cellular toxicity in a widevariety of tissues. The fold difference between efficacy in models andmammalian cell cytotoxicity provides a rough therapeutic index (TI). Insome embodiments, there is >50-fold TI for KIRAs that are tested invivo.

In vivo PK/ADMET studies: KIRAs that are sufficiently potent in thecellular assays are subjected to pharmacokinetic and toxicity studies inmice. First, compounds are tested in a dose escalation study for anyobserved toxicity. Mice are sequentially injected with single IV dosesof 1 mg/kg, 10 mg/kg, and 100 mg/kg of compound. During these singledose studies, the mice are observed for signs of acute toxicity, such asrespiratory or neurological abnormalities. Compounds that are not toxicat 10 mg/kg are subjected to PK/ADME testing. This involvesadministration of a single dose (10 mg/kg by IV) followed by bloodsampling at intervals of 30, 60, 120, 180, 240, and 300 minutes. Theseexperiments are performed with groups of 3 mice per KIRA. Plasma isseparated and extracted with acetonitrile for compound concentrationmeasurements by combined liquid chromatography/electrospray-ionizationmass spectrometry (LCMS). The results provide the maximum concentration(C_(max)), time of maximum concentration (T_(max)), area under the curve(AUC), and an estimation of half-life (T₂). Compounds that demonstratesufficient exposure are candidates for the in vivo efficacy studiesdescribed herein.

18. Inhibitors of IRE1α Kinase/Endoribonuclease to Treat RetinitisPigmentosa

KIRAs inhibit IRE1α in cultured cells at concentrations of less than 100nM and strikingly protect cell viability and function under conditionsof ER stress. Moreover, the leading compound in this class has shownefficacy in a rodent model of RP caused by mutation in rhodopsin.Described herein is the optimization of potency and efficacy in the KIRAclass of compounds against retinal degeneration to develop a clinicalcandidate for treatment of RP.

19. Allosteric Modulation of the IRE1α RNase with Novel KinaseInhibitor.

KIRA6, a more potent version of earlier KIRAs, whose structure is shownin FIG. 30A has been developed. This compound dose-dependently reduceskinase autophosphorylation and XBP1 splicing activity of IRE1α* (WT)(FIG. 30B-C). In addition, KIRA6 dose-dependently inhibits IRE1α* (WT)cleavage of pre-miR-17 (FIG. 31D).

20. Intravitreal Injections of Small Molecules

Based on known rat vitreous volumes, 2 μl was injected intravitreallyinto each eye. Tm (20 μg/μL final concentration) plus/minus KIRA6 (10 μMfinal concentration) was injected into SD rats at P21 with an equivalentamount of DMSO as a vehicle control. Retinas were collected at 48 and 72hrs after injections in Trizol (Invitrogen) for qPCR analysis. Eyes wereexamined by optical coherence tomography (OCT) 7 days post injection andsubsequently collected for morphological analysis. P23H rats wereinjected with KIRA6 (10 μM final concentration) or DMSO vehicle controlat P9 and P15, and eyes were examined at P40 by OCT, and morphologicalanalysis.

21. Image Guided Optical Coherence Tomography (OCT)

Mice were anaesthetized with 1.5-3% isoflurane, eyes were dilated with2.5% phenylephrine hydrochloride and 1% tropicamide, and corneas werekept moist with regular application of 2.5% methylcellulose. Eyes wereexamined using a Micron III retinal imaging system (Phoenix ResearchLabs). Spectral domain OCT images were acquired with a Micron ImageGuided OCT System (Phoenix Research Labs) by averaging 10 to 50 scans.

22. Morphological Analysis of Retinas

Outer nuclear layers (ONL) were quantified as previously described(Lewin, A. S. et al., Nature medicine 4, 967-971 (1998)). Briefly, ratswere euthanized by CO₂ inhalation and their eyes were immediatelyenucleated and immersed in 2% paraformaldehyde and 2.5% glutaraldehydein phosphate buffered saline. Subsequently, eyes were bisected on thevertical meridian through the optic nerve head and embedded inEpon-Araldite resin; 1 μm sections were cut and stained with toluidineblue. ONL thickness was measured at 54 locations around the retina usingBioquant image analysis (Bioquant; R&M Biometrics).

SEQ ID NO: 1 MSYYHHHHHHDYDIPTTENLYFQGAMDPE hq qqqlqhqqfq 480kelekiqllq qqqqqlpfhp pgdtaqdgel ldtsgpyses sgtsspstsp rasnhslcsg 540ssaskagssp sleqddgdee tsvvivgkis fcpkdvlghg aegtivyrgm fdnrdvavkr 600ilpecfsfad revqllresd ehpnviryfc tekdrqfqyi aiglcaatlq eyveqkdfah 660lglepitllq qttsglahlh slnivhrdlk phnilismpn ahgkikamis dfglckklav 720grhsfsrrsg vpgtegwiap emlsedcken ptytvdifsa gcvfyyvise gshpfgkslq 780rganillgac sldclhpekh edviarelie kmiamdpqkr psakhvlkhp ffwslekqlq 840ffqdvsdrie kesldgpivk qlerggravv kmdwrenitv plqtdlrkfr tykggsvrdl 900lramrnkkhh yrelpaevre tlgslpddfv cyftsrfphl lahtyramel csherlfqpy 960yfheppepqp pvtpdal SEQ ID NO: 2 hq qqqlqhqqfq 480kelekiqllq qqqqqlpfhp pgdtaqdgel ldtsgpyses sgtsspstsp rasnhslcsg 540ssaskagssp sleqddgdee tsvvivgkis fcpkdvlghg aegtivyrgm fdnrdvavkr 600ilpecfsfad revqllresd ehpnviryfc tekdrqfqyi aielcaatlq eyveqkdfah 660lglepitllq qttsglahlh slnivhrdlk phnilismpn ahgkikamis dfglckklav 720grhsfsrrsg vpgtegwiap emlsedcken ptytvdifsa gcvfyyvise gshpfgkslq 780rqanillgac sldclhpekh edviarelie kmiamdpqkr psakhvlkhp ffwslekqlq 840ffqdvsdrie kesldgpivk qlerggravv kmdwrenitv plqtdlrkfr tykggsvrdl 900lramrnkkhh yrelpaevre tlgslpddfv cyftsrfphl lahtyramel csherlfqpy 960yfheppepqp pvtpdal

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

1-69. (canceled)
 70. A compound of formula (I):

wherein: ring A is R⁴¹-substituted or unsubstituted arylene, orR⁴¹-substituted or unsubstituted heteroarylene; L¹ is a bond; L² is—NR^(6a)—; R¹ is —S(O)R¹⁰; R² is hydrogen, halogen, —CX^(a) ₃, —CN,R¹⁴-substituted or unsubstituted alkyl, R¹⁴-substituted or unsubstitutedheteroalkyl, R¹⁴-substituted or unsubstituted cycloalkyl, orR¹⁴-substituted or unsubstituted heterocycloalkyl; each R³ isindependently hydrogen, halogen, —CX^(b) ₃, —CN, —S(O)₂R^(10b),—S(O)_(n2)NR^(7b)R^(8b), —N(O)_(m2), —NR^(7b)R^(8b), —C(O)R^(9b),—C(O)OR^(9b), —C(O)NR^(7b)R^(8b), —OR^(10b), —NR^(7b)S(O)_(n2)R^(10b),—NR^(7b)C(O)R^(9b), —NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —OCX^(b) ₃,—OCHX^(b) ₂, R¹⁷-substituted or unsubstituted alkyl, R¹⁷-substituted orunsubstituted heteroalkyl, R¹⁷-substituted or unsubstituted cycloalkyl,or R¹⁷-substituted or unsubstituted heterocycloalkyl; R⁴ is hydrogen orunsubstituted C₁-C₆ alkyl; R⁵ is hydrogen or unsubstituted C₁-C₆ alkyl;R^(6a) is hydrogen, R^(26a)-substituted or unsubstituted alkyl,R^(26a)-substituted or unsubstituted heteroalkyl, R^(26a)-substituted orunsubstituted cycloalkyl, or R^(26a)-substituted or unsubstitutedheterocycloalkyl; R¹⁰ is substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, substituted or unsubstituted benzyl, or substitutedor unsubstituted heteroaryl; wherein the substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, substituted benzyl, or substituted heteroaryl issubstituted with one or more substituents independently selected fromthe group consisting of halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —NO₂, —SH, —S(O)₂Cl, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂,—NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃,—OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl, unsubstitutedheteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,unsubstituted aryl, unsubstituted benzyl, or unsubstituted heteroaryl;R^(7b), R^(8b), R^(9b) and R^(10b) are each independently hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; wherein the substituted alkyl,substituted heteroalkyl, substituted cycloalkyl, substitutedheterocycloalkyl, substituted aryl, or substituted heteroaryl issubstituted with one or more substituents independently selected fromthe group consisting of halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —NO₂, —SH, —S(O)₂C, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂,—NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃,—OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl, unsubstitutedheteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,unsubstituted aryl, or unsubstituted heteroaryl; or R^(7b) and R^(8b),together with the nitrogen atom to which they are bonded, form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl, wherein the substituted heterocycloalkyl orsubstituted heteroaryl is substituted with one or more substituentsindependently selected from the group consisting of halogen, —CF₃, —CN,—OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂C, —S(O)₃H, —S(O)₂NH₂,—NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH,—NHOH, —OCF₃, —OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl,unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstitutedheterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; eachR¹⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, —OCHF₂, R¹⁵-substituted orunsubstituted alkyl, R¹⁵-substituted or unsubstituted heteroalkyl,R¹⁵-substituted or unsubstituted cycloalkyl, R¹⁵-substituted orunsubstituted heterocycloalkyl; each R¹⁵ is independently oxo, halogen,—CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, or—OCHF₂; each R¹⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂,—C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂Cl, —S(O)₃H, —S(O)₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCF₃, —OCHF₂, R¹⁸-substituted or unsubstituted alkyl, R¹⁸-substitutedor unsubstituted heteroalkyl, R¹⁸-substituted or unsubstitutedcycloalkyl, R¹⁸-substituted or unsubstituted heterocycloalkyl,R¹⁸-substituted or unsubstituted aryl, or R¹⁸-substituted orunsubstituted heteroaryl; each R¹⁸ is independently oxo, halogen, —CF₃,—CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂Cl, —S(O)₃H,—S(O)₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCF₃, —OCHF₂, R¹⁹-substituted or unsubstituted alkyl,R¹⁹-substituted or unsubstituted heteroalkyl, R¹⁹-substituted orunsubstituted cycloalkyl, R¹⁹-substituted or unsubstitutedheterocycloalkyl, R¹⁹-substituted or unsubstituted aryl, orR¹⁹-substituted or unsubstituted heteroaryl; each R¹⁹ is independentlyoxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH,—S(O)₂C, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂,—NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃, —OCHF₂, unsubstitutedalkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl,unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstitutedheteroaryl; each R^(26a) is independently halogen, —CF₃, —CN, —OH, —NH₂,—C(O)OH, —C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, or —OCHF₂; each R⁴¹ isindependently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂,—NO₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, —OCHF₂, R⁴²-substituted orunsubstituted alkyl, R⁴²-substituted or unsubstituted heteroalkyl,R⁴²-substituted or unsubstituted cycloalkyl, or R⁴²-substituted orunsubstituted heterocycloalkyl; each R⁴² is independently oxo, halogen,—CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —S(O)₃H, —S(O)₂NH₂,—OCF₃, or —OCHF₂; each occurrence of X^(a) and X^(b) is independentlyhalogen; each occurrence of m2 is independently 1 or 2; each occurrenceof n and n2 is independently 0, 1, or 2; each occurrence of v2 isindependently 1 or 2; and z is 0, 1, or 2; or a pharmaceuticallyacceptable salt thereof.
 71. The compound of claim 70, wherein ring A isR⁴¹-substituted or unsubstituted phenylene.
 72. The compound of claim70, wherein ring A is R⁴¹-substituted or unsubstituted naphthylene. 73.The compound of claim 70, wherein R^(6a) is H.
 74. The compound of claim70, wherein n is
 2. 75. The compound of claim 70, wherein R¹⁰ issubstituted or unsubstituted alkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted phenyl, substituted orunsubstituted naphthyl, substituted or unsubstituted benzyl, orsubstituted or unsubstituted heteroaryl.
 76. The compound of claim 70,wherein R¹⁰ is substituted or unsubstituted phenyl, or substituted orunsubstituted benzyl.
 77. The compound of claim 70, wherein R² isR¹⁴-substituted or unsubstituted alkyl, or R¹⁴-substituted orunsubstituted cycloalkyl.
 78. The compound of claim 70, wherein z is 0.79. The compound of claim 70, wherein R⁴ is hydrogen and R⁵ is hydrogen.80. A pharmaceutical composition comprising a pharmaceuticallyacceptable excipient and a compound of claim 70, or a pharmaceuticallyacceptable salt thereof.
 81. A method of modulating activity of aninositol-requiring enzyme (Ire1) protein in a subject, the methodcomprising administering to the subject a therapeutically effectiveamount of a compound of formula (I):

wherein: ring A is R⁴¹-substituted or unsubstituted arylene, orR⁴¹-substituted or unsubstituted heteroarylene; L¹ is a bond; L² is—NR^(6a)—; R¹ is —S(O)_(n)R¹⁰; R² is hydrogen, halogen, —CX^(a) ₃, —CN,R¹⁴-substituted or unsubstituted alkyl, R¹⁴-substituted or unsubstitutedheteroalkyl, R¹⁴-substituted or unsubstituted cycloalkyl, orR¹⁴-substituted or unsubstituted heterocycloalkyl; each R³ isindependently hydrogen, halogen, —CX^(b) ₃, —CN, —S(O)_(n2)R^(10b),—S(O)_(v2)NR^(7b)R^(8b), —N(O)_(m2), —NR^(7b)R^(8b), —C(O)R^(9b),—C(O)OR^(9b), —C(O)NR^(7b)R^(8b), —OROb, —NR^(7b)S(O)_(n2)R^(10b),—NR^(7b)C(O)R^(9b), —NR^(7b)C(O)OR^(9b), —NR^(7b)OR^(9b), —OCX^(b) ₃,—OCHX^(b) ₂, R¹⁷-substituted or unsubstituted alkyl, R¹⁷-substituted orunsubstituted heteroalkyl, R¹⁷-substituted or unsubstituted cycloalkyl,or R¹⁷-substituted or unsubstituted heterocycloalkyl; R⁴ is hydrogen orunsubstituted C₁-C₆ alkyl; R⁵ is hydrogen or unsubstituted C₁-C₆ alkyl;R^(6a) is hydrogen, R^(26a)-substituted or unsubstituted alkyl,R^(26a)-substituted or unsubstituted heteroalkyl, R^(26a)-substituted orunsubstituted cycloalkyl, or R^(26a)-substituted or unsubstitutedheterocycloalkyl; R¹⁰ is substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, substituted or unsubstituted benzyl, or substitutedor unsubstituted heteroaryl; wherein the substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, substituted benzyl, or substituted heteroaryl issubstituted with one or more substituents independently selected fromthe group consisting of halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —NO₂, —SH, —S(O)₂Cl, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂,—NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃,—OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl, unsubstitutedheteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,unsubstituted aryl, unsubstituted benzyl, or unsubstituted heteroaryl;R^(7b), R^(8b), R^(9b) and R^(10b) are each independently hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; wherein the substituted alkyl,substituted heteroalkyl, substituted cycloalkyl, substitutedheterocycloalkyl, substituted aryl, or substituted heteroaryl issubstituted with one or more substituents independently selected fromthe group consisting of halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —NO₂, —SH, —S(O)₂C, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂,—NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃,—OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl, unsubstitutedheteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl,unsubstituted aryl, or unsubstituted heteroaryl; or R^(7b) and R^(8b),together with the nitrogen atom to which they are bonded, form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl, wherein the substituted heterocycloalkyl orsubstituted heteroaryl is substituted with one or more substituentsindependently selected from the group consisting of halogen, —CF₃, —CN,—OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂C, —S(O)₃H, —S(O)₂NH₂,—NHNH₂, —ONH₂, —NHC(O)NIHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCF₃, —OCHF₂, —NHS(O)₂CH₃, —N₃, unsubstituted alkyl,unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstitutedheterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl; eachR¹⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH,—C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, —OCHF₂, R¹⁵-substituted orunsubstituted alkyl, R¹⁵-substituted or unsubstituted heteroalkyl,R¹⁵-substituted or unsubstituted cycloalkyl, R¹⁵-substituted orunsubstituted heterocycloalkyl; each R¹⁵ is independently oxo, halogen,—CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, or—OCHF₂; each R¹⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂,—C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂Cl, —S(O)₃H, —S(O)₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCF₃, —OCHF₂, R¹⁸-substituted or unsubstituted alkyl, R¹⁸-substitutedor unsubstituted heteroalkyl, R¹⁸-substituted or unsubstitutedcycloalkyl, R¹⁵-substituted or unsubstituted heterocycloalkyl,R¹⁵-substituted or unsubstituted aryl, or R¹⁵-substituted orunsubstituted heteroaryl; each R¹⁸ is independently oxo, halogen, —CF₃,—CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH, —S(O)₂C, —S(O)₃H,—S(O)₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHS(O)₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCF₃, —OCHF₂, R¹⁹-substituted or unsubstituted alkyl,R¹⁹-substituted or unsubstituted heteroalkyl, R¹⁹-substituted orunsubstituted cycloalkyl, R¹⁹-substituted or unsubstitutedheterocycloalkyl, R¹⁹-substituted or unsubstituted aryl, orR¹⁹-substituted or unsubstituted heteroaryl; each R¹⁹ is independentlyoxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —SH,—S(O)₂Cl, —S(O)₃H, —S(O)₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂,—NHS(O)₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —OCF₃, —OCHF₂, unsubstitutedalkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl,unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstitutedheteroaryl; each R^(26a) is independently halogen, —CF₃, —CN, —OH, —NH₂,—C(O)OH, —C(O)NH₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, or —OCHF₂; each R⁴¹ isindependently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂,—NO₂, —S(O)₃H, —S(O)₂NH₂, —OCF₃, —OCHF₂, R⁴²-substituted orunsubstituted alkyl, R⁴²-substituted or unsubstituted heteroalkyl,R⁴²-substituted or unsubstituted cycloalkyl, or R⁴²-substituted orunsubstituted heterocycloalkyl; each R⁴² is independently oxo, halogen,—CF₃, —CN, —OH, —NH₂, —C(O)OH, —C(O)NH₂, —NO₂, —S(O)₃H, —S(O)₂NH₂,—OCF₃, or —OCHF₂; each occurrence of X^(a) and X^(b) is independentlyhalogen; each occurrence of m2 is independently 1 or 2; each occurrenceof n and n2 is independently 0, 1, or 2; each occurrence of v2 isindependently 1 or 2; and z is 0, 1, or 2; or a pharmaceuticallyacceptable salt thereof.
 82. The method of claim 81, wherein the subjectsuffers from a disease selected from the group consisting of cancer,diabetes, demyelinating disease, eye disease, fibrotic disease, andneurodegenerative disease.
 83. The method of claim 82, wherein theneurodegenerative disease is retinitis pigmentosa, amyotrophic lateralsclerosis, retinal degeneration, macular degeneration, Parkinson'sDisease, Alzheimer Disease, Huntington's Disease, Prion Disease,Creutzfeldt-Jakob Disease, or Kuru.
 84. The method of claim 82, whereinthe demyelinating disease is Wolfram Syndrome, Pelizaeus-MerzbacherDisease, Transverse Myelitis, Charcot-Marie-Tooth Disease, or MultipleSclerosis.
 85. The method of claim 82, wherein the cancer is multiplemyeloma.
 86. The method of claim 82, wherein the diabetes is type I ortype II diabetes.
 87. The method of claim 82, wherein the eye disease isretinitis pigmentosa, retinal degeneration, macular degeneration, orWolfram Syndrome.
 88. The method of claim 82, wherein the fibroticdisease is idiopathic pulmonary fibrosis (IPF), myocardial infarction,cardiac hypertrophy, heart failure, cirrhosis, acetominophen (Tylenol)liver toxicity, hepatitis C liver disease, hepatosteatosis (fatty liverdisease), or hepatic fibrosis.